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The Second Alliance-PLANT War is the main conflict of the anime Mobile Suit Gundam SEED Destiny. It is a conflict between PLANT and Earth Alliance forces that began with "Break the World" Incident in C.E. 73. However, the Alliance was later thrown into chaos by PLANT Supreme Council Chairman Gilbert Durandal's declaration to overthrow Logos, so the war did not turn into a total war between the Natural and Coordinator factions like the First Alliance-PLANT War. Despite this, both Earth and PLANT suffered more damage than in the previous war.

Prelude[]

Following the climatic Second Battle of Jachin Due, in which the extremists of the Earth Alliance and PLANT sought to annihilate each other with nuclear weapons, a ceasefire was established by the Moderate Faction, and negotiations to end the war soon took place.[1] During the intervening six months of negations, a group of former ZAFT soldiers loyal to the ideals of Patrick Zala attempted to reignite the war by attacking both the PLANT Provisional Chairman Eileen Canaver, and the Nairobi Peace Conference. However, these groups were ultimately stoped by the combined forces of the Three Ships Alliance and Orb Union.[2] On March 10, C.E. 72, the First Alliance-PLANT War officially with the signing of the Junius Treaty.[3]

The Junius Treaty granted the PLANT Colonies autonomy from the Earth Alliance, and returned political power and territories, taken by the Earth Alliance during the war from neutral nations and the United States of South America, to their respective governments. The treaty also included the Lindeman Plan sub-clause, which stipulated several restrictions on military affair, including: limiting the numbers of warships and mobile suits that a nation could maintain based on national power, and the outright banning of nuclear weapons, Neutron Jammers, Neutron Jammer Cancellers, and Mirage Colloid technology for military use.[4] ZAFT, PLANT's military organization, also provided N-Jammer Cancellers to the Earth Alliance to solve its energy crisis, caused by April's Fool Crisis on Earth, in which ZAFT buried N-Jammers deep underground to prevent any further nuclear attacks on PLANT, as well as killing millions of people on Earth that were completely reliant on nuclear energy found themselves without electricity.

The Junius Treaty failed to ban the anti-Coordinator factions on Earth. Thus, in those two years, one of the primary forces behind the war, the ruling extremist Earth Alliance organization Blue Cosmos, reorganized under the leadership of Lord Djibril and continued to exercise influence over Earth's political elite.

The peace treaty notwithstanding, both PLANT and the Earth Alliance continued to expand their military assets, including the development of new mobile suits. Although nuclear technologies were banned, some remained secretly on both sides' development agendas.

Chronology[]

Precursor Incidents[]

Attack on Armory One (October 2, C.E. 73)[]

With both PLANT/ZAFT and Earth Alliance members building up their military powers, Orb Union representative Cagalli Yula Athha arranged a meeting with PLANT Chairman Gilbert Durandal to discuss the need for power in the post-war era. Athrun Zala accompanied her as her bodyguard, under the alias "Alex Dino". The meeting took place at ZAFT's industrial colony Armory One, which was currently preparing for the launch ceremony of the first post-war battleship, the LHM-BB01 Minerva.

While Cagalli met with Durandal, Earth Alliance pilots Sting Oakley, Auel Neider, and Stella Loussier infiltrated the base thanks to ZAFT spies, commandeered ZAFT's newest Gundam-type mobile suits, the ZGMF-X24S Chaos Gundam, ZGMF-X31S Abyss Gundam, and ZGMF-X88S Gaia Gundam, respectively, and heavily damaged the installation as they attempted to escape the base with their stolen machines.

Immediately, various ZAFT mobile suits engaged the three units, including the new mass-production ZAKU Warrior/Phantom units and the ZGMF-X56S Impulse Gundam, piloted by Shinn Asuka, as well as the crew of the Minerva. The stolen units, however, successfully escaped the colony and were picked up by the Mirage Colloid-cloaked Earth Alliance battleship Girty Lue, waiting just outside the colony.

The Minerva launched and chased the Girty Lue, engaging in battle several times. The chase was interrupted when the Minerva was involved in the upcoming which would become known as Operation "Break the World".

"Break The World" Incident (October 3)[]

The theft of the three Gundams was immediately set aside when unusual movement was detected from the wreckage of the destroyed Junius Seven colony, which was supposed to be in a stable orbit. A Patrick Zala-loyalist rogue ZAFT force piloting ZGMF-1017M2 GINN High Maneuver Type II units, planted engines all over the wreckage, sending it on a collision course with Earth.

A ZAFT squadron under the command of Yzak Joule was dispatched to break up the wreckage, and was soon reinforced by the approaching Minerva's mobile suits. They were engaged in battle with the rogue squadron, who (mostly) easily outperformed the members of the Joule team, and operations to break the wreckage into pieces were compromised. The Girty Lue also arrived on the scene, launched the stolen mobile suit units and engaged the Minerva, further hampering operations (possibly intentionally, so Blue Cosmos could start another war).

The Minerva's forces successfully broke the wreckage of Junius Seven into half with its Tannhäuser positron blaster cannon just as it began entering the upper atmosphere. As the two pieces entered the atmosphere, the Girty Lue and the survivors of the Joule team withdrew, but the Minerva decided to stay and continued to destroy the debris, breaking it into smaller fragments with its Tannhäuser. The destruction was however insufficient, and the remaining pieces landed on Earth, destroying Athens, Philadelphia, Quebec, part of the Great Wall of China, Shanghai, Rome, Prague, and numerous other locations, while pieces that hit the sea caused massive tsunami and tidal waves. The most severe damage occurred near the equator.

An alliance of the Junk Guild, Serpent Tail and Rondo Mina Sahaku attempted to use GENESIS Alpha to stop the wreckage of Junius Seven, but the operation failed due to the intervention of the RGX-00 Testament Gundam.

In the aftermath of the disaster, PLANT/ZAFT immediately sent humanitarian aid to Earth. Lord Djibril, the new leader of anti-Coordinator group Blue Cosmos, took advantage of the incident and divulged photographic evidence showing the rogue ZAFT units executing the drop, and started to manipulate the public opinion into blaming Coordinators for the disaster. He also used his position within the secret society Logos to influence or even directly command the president of the Atlantic Federation, Joseph Copeland, to start another war against PLANT.

Declaration of War[]

Fueled by public opinion, manipulated by Blue Cosmos, Copeland sent a list of demands to PLANT Supreme Council. PLANT was blamed for harboring the terrorists that had committed the drop, even though all had been killed. The demands required PLANT to dismantle its military, dismiss the current PLANT Supreme Council, and to submit to Earth Alliance inspectors.

Durandal wished to find a diplomatic solution, but the Earth military had already begun deploying forces and PLANT was forced to man its defense line. Before the expiration of the ultimatum, the Earth Alliance attacked PLANT, officially starting the Second Alliance-PLANT War.

Battle of Aprilius One (November)[]

The Earth Alliance main force launched its battleships and mobile suits against the PLANT homeland, which managed to repel the attack. Meanwhile, a separate ambush team moved to attack Aprilius One, the location of the PLANT Supreme Council. The team launched a squadron of new GAT-04 Windam units carrying nuclear missile launchers, but fortunately, a scout unit located the squadron in time. Knowing that it was very likely the Earth Alliance might try to use nuclear missiles, a Nazca-class vessel was equipped with a Neutron Stampeder and stationed on standby to protect the PLANTs from this type of scenario. When the Stampeder was activated, it sent out high frequency radiation that detonated all the nuclear weapons in the ambush fleet, which was completely destroyed by their own prematurely detonating missiles. Having failed in their mission to destroy the PLANTs with a nuclear strike, the Earth Alliance forces withdrew.

As the nuclear devices detonated in proximity of the colonies, PLANT's citizens were outraged and began pushing for a retaliatory strike against all Naturals. Durandal, knowing of the possible escalation of the conflict, used the help of a Lacus Clyne body double, Meer Campbell, to calm the people.

Durandal then assigned the ZGMF-X23S Saviour Gundam to Athrun, who had re-enlisted in ZAFT. He also appointed Athrun to FAITH, a special forces unit reporting directly to Durandal, effectively given permission to use his power as his conscience dictated. As requested by Durandal, Athrun soon departed for Earth to join the Minerva and notify captain Talia Gladys about her own appointment to FAITH.

Operation Spear of Twilight[]

Following the Earth Alliance's failed nuclear attack, ZAFT's Defense Committee drafted a series of proposals meant to strengthen ZAFT's position. Earth Alliance forces had begun surrounding ZAFT Earth bases at Gibraltar and Carpentaria, but the surprise use of the Neutron Stampeder stalled the Earth Alliance forces. ZAFT forces gathered in the atmosphere to commence a drop operation to support Gibraltar and Carpentaria, and although they met a fierce opposition from the remaining Earth Alliance forces stationed on the moon, they defeated the Earth Alliance forces that were surrounding their bases.

Orb Enters into the Earth Alliance[]

Declaration to Sign into the World Security Treaty Organization[]

Under pressure from public opinion, now fiercely against ZAFT, the Earth Alliance sought an alliance with Orb, which possessed a technically advanced and powerful military force.

The majority faction of Orb's governing body, led by Prime Minister Unato Ema Seiran and his son Yuna Roma Seiran, supported an alliance. Cagalli, Orb's representative, remained fiercely opposed. The council feared the Atlantic Federation's military strength, and wanted to avoid the events of the first war, when neutral Orb was attacked by the Earth Alliance and suffered massive casualties. Cagalli was eventually manipulated into accepting the alliance, mostly by the arguments that 'Orb cannot be burned again' and that they would be forced to withdraw the humanitarian aid they were extending to the victims of the Break the World incident.

Had Orb's original leadership not sacrificed itself during the first war, Orb may not have joined the Earth Alliance. Instead, Orb declared it would sign into the World Security Treaty Organization.

Ambush of the Minerva[]

Orb's council planned to give the Minerva to the Earth Alliance as a gift of good faith. The Minerva was still docked in Orb, after the damage she took in the battle around the drop of Junius Seven.

Warned by Andrew Waltfeld, the ship departed immediately from Orb, but was ambushed by a vast Earth Alliance fleet as soon as it left Orb territorial waters. The Earth Alliance deployed the massive mobile armor YMAF-X6BD Zamza-Zah, equipped with a Positron Reflector. An Orb fleet was deployed on the border to prevent the Minerva from retreating into its territory.

Despite the odds, the Minerva successfully escaped the ambush by laying waste to the opposing fleet, destroying the mobile armor and sinking several carrier ships. The new Deuterion Beam Energy Transfer System and Shinn's SEED factor were instrumental in the battle. The damaged Minerva headed for the ZAFT Carpentaria base in Australia.

Assassination Attempt of Lacus Clyne (December)[]

After the First Alliance-PLANT War, the main figures of the Clyne Faction lived secretly at Reverend Malchio's orphanage in Orb, hiding both the LCAM-01XA Archangel as well as the secretly repaired ZGMF-X10A Freedom Gundam.

An unknown commando task force of Coordinators attempted to assassinate Lacus Clyne at the orphanage, but all of them were incapacitated by the Freedom when they used their mobile suits to attack the bunker everyone had evacuated to. All the pilots killed themselves by self-destructing their mobile suits shortly after being defeated to avoid interrogation. The fact that the commandos were Coordinators and that they were piloting the new ZAFT aquatic unit UMF/SSO-3 ASH (then only available to elite units) suggested the team was from ZAFT. It was then thought that the assassination was ordered by Durandal, in order to replace Lacus with Meer.

As a result of the attack, and after the recent political events, some of the remaining Archangel crew assembled and launched the ship, departing from Orb and hiding underwater.

Kidnapping of Orb's Chief Representative (December)[]

Before leaving Orb, a letter was delivered to Kira Yamato from Cagalli stating her intentions to marry Yuna Roma Seiran in support of Orb joining the Earth Alliance, along with the ring given to her by Athrun. Concerned for her in her present state-of-mind and in her future with Orb, Kira launched in the Freedom from the emerging Archangel towards Orb's main island, where the wedding was taking place. There, the Freedom interrupted the ceremony by disarming MVF-M11C Murasame and MBF-M1 Astray units present, briefly landing at the base of the altar, grabbed Cagalli, and immediately took off returning to the Archangel.

As the Freedom approached the Archangel, Orb Naval Patrol Ships learned of Cagalli's kidnapping by the Freedom, but since Cagalli was now inside the Freedom's cockpit, the ships refused to fire on the mobile suit for fear of harming her. Nevertheless, the Freedom enters the Archangel, and the ship again submerged into the ocean: as it did, Orb captain Todaka saluted, praying for the Archangel to protect Cagalli in their place.

With Cagalli's absence, Yuna assumed the position of Orb's Representative and Commander-in-Chief. Orb signed the World Security Treaty, officially joining the Earth Alliance.

Battle of the Indian Ocean[]

Battle of Gulnahan[]

On route to the Black Sea ZAFT base, the Minerva had to break through Earth Alliance forces stationed in the Middle East area. With the help of local guerilla units, the Minerva managed to destroy a land-based Lohengrin positron cannon fortification in the Gulnahan ravine, east of Suez. The cannon had previously been unassailable thanks to the new YMAG-X7F Gells-Ghe mobile armor and its positron reflector. The destruction of the fortification, which had become known as the "Lohengrin Gate", resulted in the liberation of the nearby city which had been occupied and oppressed by EA forces. The locals quickly repaid the brutality and cruelty that had been shown to them by the EA and executed numerous captured EA soldiers and officers.

Battle of Dardanelles[]

En route to the ZAFT's Gibraltar base, the Minerva departed from ZAFT base in the Black Sea, but was intercepted by an Earth Alliance fleet in the Strait of Dardanelles. Despite the Orb Union's historical non-aggression policy, and in light of the new treaty with the Earth Alliance, Orb couldn't refuse orders from the Earth Alliance and a massive fleet comprised of several carriers containing numerous Murasame units engaged the Minerva.

Soon after, as the Minerva was about to fire its Tannhäuser at the leading Orb ship, the cannon was destroyed by the Freedom Gundam, piloted by Kira, killing several crewmen from the Minerva in the process. The intervention of the Archangel stalled the battle, and Cagalli in her MBF-02+AQM/E-X01 Aile Strike Rouge (MBF-02+EW454F Strike Rouge Ootori in the HD Remaster) tried to talk Orb pilots out from attacking the Minerva. Her attempt failed as Yuna declared her to be an impostor and ordered the leading Orb ship to fire on Cagalli's Strike Rouge and on the Archangel.

After Orb committed itself to the battle, the Earth Alliance fleet also joined in, contributing the three Gundam units stolen at Armory One, as well as a number of Windams. The Minerva, in response, sortied its three remaining mobile suits, a custom-colored ZGMF-1000/A1 Gunner ZAKU Warrior piloted by Lunamaria Hawke, a ZGMF-1001/M Blaze ZAKU Phantom piloted by Rey Za Burrel, and the prototype ZGMF-X2000 GOUF Ignited piloted by FAITH member Heine Westenfluss, to back up Shinn's ZGMF-X56S/α Force Impulse Gundam and Athrun's Saviour, both of which had already sortied to defend the ship. The fighting was fierce, with the Archangel and the Freedom trying to carefully launch attacks designed to deter combat between mobile suits and disable aggressive units. Kira's Freedom quickly damages Shinn's Force Impulse, and effortlessly disables or cripples Heine'sGOUF Ignited, Stella's Gaia, and Auel's Abyss. In anger at the Freedom's domination of the battle and at being damaged by the Freedom, Heine and Stella both moved to attack the Freedom and the GOUF Ignited unknowingly moved in between the two as Stella charges towards Kira - Heine and his GOUF Ignited were sliced in half by the Gaia on its way. Kira notices the attack and kicks Stella away.

The Earth Alliance eventually disengaged the battle after most of their mobile suits were destroyed or disabled. The Orb fleet was also forced to withdraw from the battle, mostly because of the same reason.

Lacus Clyne Shuttle Hijacking[]

Battle of Crete[]

The Minerva reprised its route towards Gibraltar, only to be intercepted again by the same Orb naval fleet under the orders of captain Todaka and Yuna Roma Seiran. The Archangel, together with the Freedom and the Strike Rouge, unsuccessfully tried again to stop the Orb forces by disabling various units and ordering their withdrawal. The Alliance naval fleet under the command of Neo Roanoke also participated in the battle, closing the Minerva in a pincher move.

The Abyss and Chaos engaged the Impulse and Saviour respectively. Left with only two mobile suits that were limited in mobility to the ship's upper deck as cover, the Minerva was attacked by the entire Orb mobile suit force, consisting of several attack groups of Murasame units. The attack was repelled, but the Minerva was heavily damage. While defending the ship, Rey's Blaze ZAKU Phantom was slightly damaged and Lunamaria's Gunner ZAKU Warrior was badly damaged. Athrun's Saviour was damaged beyond repair by Kira's Freedom in a duel between the two; all three Minerva pilots survived, though Lunamaria had to receive medical attention from her injuries.

While Kira was battling Athrun, Shinn destroyed the Abyss, killing Auel. Shinn then decimated the Orb mobile suit force, and after that, he directly engaged the Orb fleet, sinking several ships. The Orb flagship aircraft carrier Takemikazuchi launched a frontal attack on the Minerva, but under fire from the Minerva's main cannons and after a killing blow from the Sword Impulse, it exploded and sank before reaching the Minerva. Captain Todaka valiantly chose to go down with his ship, but he ordered his most loyal crewmembers to join the Archangel and fight for Orb's true ideals, rather than returning to the Earth Alliance.

The Destroy Crisis - Battle of Berlin[]

After losing the Gaia to the Minerva, Neo Roanoke was assigned the massive mobile suit GFAS-X1 Destroy Gundam by Lord Djibril, and designates Stella as its pilot. She then went on a rampage and used it to completely destroy several cities in Western Eurasia - former Eurasian Federation territories that had sided with ZAFT - in addition to all ZAFT forces that engaged the Destroy, to show the rest of the Earth Alliance what would happen if any of them sided with ZAFT.

The Destroy Gundam was intercepted once more by ZAFT over the city of Berlin. The ZAFT units were no match for the Destroy's massive and numerous energy weapons as well as its multiple positron reflectors, and Berlin was heavily damaged while ZAFT forces in Berlin were utterly obliterated. Soon after, the Archangel and its complement of mobile suits (including a group of Murasames from the Takemikazuchi) arrived and commenced battle against the Destroy, much to the surprise of the ZAFT ship Minerva, which arrived shortly afterwards.

Kira in the Freedom engaged the Destroy and was later joined by Shinn in the Force Impulse, while Cagalli in the Strike Rouge and three Murasames engaged Sting in the Chaos. Both the Minerva and the Archangel provided support to their mobile suits from the rear. When the Destroy's cockpit was slashed open by Shinn, Neo signaled to him that the pilot was Stella. Shinn's feelings for her stopped him from finishing the Destroy, and Stella's feelings for Shinn caused her to stop fighting too. During this time, the Freedom came into Stella's view and she, who had been warned by Neo that the Freedom was dangerous, and seeing Neo's Windam got shot down by the Freedom, got hysterical and prepared to fire the Destroy's chest beam cannons despite Shinn being in the way. Kira then stabbed the Destroy's chest beam cannons with both beam sabers before they could fire, defeating the Destroy and mortally wounding Stella in the process.

During the battle, Sting found himself being overwhelmed by the Archangel's Murasames and chose to retreat, but sustained heavy beam fire from a trio of Murasames before he could withdraw. As his Chaos plummeted towards the ground, it was cut in half by Murasame team leader Ikeya and exploded. Sting was initially believed to be dead, but he managed to survive and was transferred to Heaven's Base.

Kira, sensing something familiar in Neo again, disabled his Windam, sending it crashing towards the ground. Archangel captain Murrue then happens to see a screen showing Neo laying unconscious without his mask, and was shocked to see that he looks like Mu La Flaga, who she thought had died during the Second Battle of Jachin Due. Elsewhere, Shinn rescued Stella from the Destroy's cockpit and tries to save her, but she dies in his arms.

At the end of the battle, Berlin was nearly destroyed, which led to increasing tension between the Atlantic and Eurasian Federations and led to the break down of the original Earth Alliance - this essentially left the Atlantic Federation to fight ZAFT on their own. And when Gilbert Durandal exposed Logos on international TV shortly after, Djibril's plan to keep Eurasia in line with the Destroy Gundam essentially backfired, as it triggered the total collapse of the Earth Alliance and more importantly, revealed the existence of Logos itself as the cause of the war. Additionally, all footage of the Archangel and the Freedom were omitted from ZAFT's television coverage during Durandal's speech to make it look like that only ZAFT came to aid the people of Berlin.

Campaign Against Logos[]

After the battle, at a news conference that was broadcast across the PLANTs and Earth, Chairman Durandal told people that there was an information gap, so he showed video footage of the war and gave a speech: He says that the Alliance's excuse was to liberate Western Eurasia from ZAFT, but asked if destruction was liberation (with the Impulse gaining credit for defeating the Destroy due to the removal of the Freedom from the video footage covering the event). Meer joined the conference and says that the war was set up by ZAFT radical extremists. Durandal says that ZAFT was supporting those who wanted to break free of the Alliance for humanitarian reasons.

He reveals to the people of Earth and the PLANTs that Logos, the secret benefactor behind the Earth Alliance had been manipulating world events and were the cause of major conflict, including the Alliance-PLANT Wars. He explained that even the Alliance's Blue Cosmos rulers were just a pawn of Logos. When he showed the photos and names of all Logos members (including Lord Djibril, who unsuccessfully ordered the broadcast to be cut off), Durandal said that Logos wanted people to fight for their profit and vowed that ZAFT would destroy Logos in order to bring peace between Earth and the PLANTs. The speech greatly strengthened Earth's support for ZAFT and weakened civilian support for the Alliance. The ZAFT campaign to destroy Logos and Blue Cosmos had begun.

The crew of the Archangel, after seeing the broadcast, decide to head back to Orb fearing it might be attacked due to the fact that Orb was affiliated with the Earth Alliance. Several Earth Alliance naval fleets defected and stationed themselves at Gibraltar shortly after the news conference.

Operation Angel Down[]

Operation "Angel Down" commenced when an AMRF-101C AWACS DINN picked up the Archangel on its sensors as the ship was traveling back to Orb. ZAFT sends the Compton-class Uhlenbeck, one of their newer model of land battleships, and its mobile suits, a compliment of TMF/A-802 BuCUEs and AMA-953 BABIs begin to attack the Archangel. The Archangel tried to escape, but sends Kira and his Freedom out to help in their defense.

The goal of the operation was to sink the Archangel and destroy the Freedom, as the ZAFT HQ claimed that they had only caused confusion in the battlefield during their previous encounters with them. The Minerva was ordered to take part in the battle. If the Archangel made it to the sea and managed to submerge, the battle would be over.

When the Minerva arrived, Shinn launches in the Force Impulse and engaged the Freedom. The Compton stopped its attacks. The Force Impulse repeatedly blocks the Freedom from defending the Archangel or running away. Before the battle, Shinn had been studying the moves of the Freedom with Rey's help, and used an array of preplanned surprise tactics to battle the Freedom.

During the battle, Minerva captain Talia tells the Archangel to surrender and they would be spared. However, Archangel captain Murrue politely refused, claiming that they only wish to return to Orb and that the ship still had things to do. At this point, the land battleship resumed its attack, claiming that Gladys was too soft.

At the climax of the battle, the Archangel begins submerging into the sea, while the Minerva fires the Tannhäuser in a last ditch attempt to stop the Archangel. Once the positron shot hits the waters, it generates a massive explosion, which damages the submerged Archangel. Murrue then orders one of the damaged engines to be jettisoned and detonated as a ruse to buy time for their escape. It was later confirmed by ZAFT's underwater search team that the Archangel had indeed escaped intact.

Around the same time, Shinn makes creative use of the Impulse's replaceable Silhouette packs, its ability to separate its body parts (and by extension, to receive replacements for damaged parts), and by taking advantage of Kira's fighting style (which primarily involves disabling the enemy MS weapons/cameras), as well as Kira's unwillingness to kill. Shinn manages to get the Freedom off balance with a "Flash Edge" beam boomerang and then impale the mobile suit in the abdomen with an "Excalibur" anti-ship laser sword from the β Sword Silhouette. Kira shut down the Freedom's nuclear reactor in the nick of time, and as a side effect, shut down the Freedom's Phase Shift Armor, and his mobile suit was torn apart when it was hit by the shock wave from the nearby explosion (caused by the Minerva's Tannhäuser shot striking the water). Shinn believed his attack had obliterated the Freedom and therefore avenged Stella's death. In truth, the shielded cockpit in the chest survived intact, and the unconscious Kira was later rescued by Cagalli piloting the Strike Rouge.

Desertion of Athrun Zala and Meyrin Hawke[]

After Operation "Angel Down", Athrun was angry that ZAFT had to destroy the Archangel as Kira was his best friend and because he believed that their motives were to reduce the bloodshed, but Durandal thinks that they have only caused confusion throughout the war. After Durandal unveils to Shinn and Athrun the nuclear-powered ZGMF-X42S Destiny Gundam and the ZGMF-X666S Legend Gundam, Durandal and Rey have a meeting and decide that Athrun's emotional attachment to the Archangel prevents him from being any more useful to their purposes, they decide to frame him as a traitor, which Meer Campbell overhears. After Meer warns him of his impending arrest, Athrun ambushes the MPs sent to arrest him.

After Meer refuses to go with him, Athrun then escapes into Meyrin Hawke's room. After Meyrin sets off a false alarm to distract the soldiers, the two escape in GOUF Ignited. However, they were found by Rey as they try to escape, and afterwards are pursued by both Shinn and Rey in the Destiny and Legend. Despite Athrun's objections to Shinn about how he is being deceived by both Durandal and Rey, Rey convinces Shinn that Athrun is unstable and Shinn ultimately impales the GOUF Ignited with the Destiny's "Arondight" anti-ship sword, sending it crashing to the sea. However, Athrun and Meyrin were rescued by Ledonir Kisaka, the former captain of Kusanagi and Cagalli's bodyguard from the first war, who was posing as an Earth Alliance officer on board one of the defecting Earth Alliance ships that was near the area where the GOUF Ignited fell. The two are transferred to the Archangel's infirmary in Orb.

Meanwhile, Durandal fabricated evidence that Athrun and Meyrin were working for Logos, and that they accessed classified information before they deserted.

Operation Ragnarök - Battle of Heaven's Base[]

ZAFT and defected Earth Alliance forces mobilize for a siege of Heaven's Base, the headquarters of the Logos benefactors of the Earth Alliance's Blue Cosmos rulers. They give them the choice of handing over the Logos members and dismantling or getting attacked. Before the time limit even expired, the ZAFT/anti-Logos Earth Alliance forces were met with resistance by a sudden barrage of rockets. Also, a great number of mobile weapons, as well as five Destroy Gundams (one unit piloted by former Chaos pilot Sting Oakley) are deployed against the joint ZAFT/anti-Logos Alliance forces. Because of this, many of the anti-Logos EA ships and mobile suits (conveniently placed near the front of the formations) are destroyed, especially by the Destroy units. Soon, ZAFT forces begin suffering casualties. In response, ZAFT launches an attack from above by dropping a great number of mobile suits from Earth's orbit. However, Logos is well prepared for this and orders the activation of the powerful Nibelung weapon, which sends out a massive energy burst (in similar fashion as the GENESIS superweapon), destroying all units coming from above and crippling the already weakened forces.

The Minerva finally launches the Destiny, Legend, and Impulse (now piloted by Lunamaria) which quickly turns the tide of the battle. Then, Lunamaria leads a group of ZAKUs, BABIs, DINNs and GOUFs against the Windams, while GOOhNs, ZnOs and ASHs take out the aquatic GAT-707E Forbidden Vortexs and shoreline defenses. Shinn and Rey attack the five Destroy units in the meantime. Shinn then tells Lunamaria to switch to the Sword Silhouette and give one Excalibur to Rey, and the three pilots then set to work eliminating the Destroys with the Destiny's Arondight and the Excalibur anti-ship swords. Sting is killed when Shinn drives his anti-ship sword into his Destroy's cockpit. In the meantime, ZAFT forces gain the upper hand when they are able to successfully penetrate the base. After Sting's Destroy unit was lost, Djibril - knowing that Heaven's Base was all but lost - abandoned the other Logos members and fled in a submarine towards Orb. The other Logos members were then captured and put on trial by both the Earth Alliance and PLANT.

Eternal Chase[]

While the Battle of Heaven's Base raged on Earth, in space another set of events are taking place. Martin DaCosta journeyed to the Mendel colony to retrieve evidence about Durandal's plans (how the Clyne Faction learned of this is unknown). While DaCosta was examining the abandoned genetics laboratory on Mendel, he discovered a research notebook which he took and returned to the Eternal (followed discreetly by a ZGMF-LRR704B GINN Long Range Reconnaissance Type). Aboard the Eternal, Lacus and Waltfeld examine the journal and ponder the meaning of the "Destiny Plan" mentioned in it; however, they are interrupted by an alarm signaling that they have been discovered by ZAFT.

Lacus immediately orders the Eternal to launch so they can try to deliver the ZGMF-X20A Strike Freedom Gundam and ZGMF-X19A ∞ Justice Gundam to the Archangel at all costs as well as to draw ZAFT away from the Clyne Faction's secret manufacturing facility Factory located nearby. As they get near Earth, they are ambushed by two more ZAFT Nazca-class ships and multiple squadrons of ZAKUs and GOUFs. Knowing that the situation is grim, Waltfeld decides to launch in the Gaia painted in his custom colors, but is gradually fighting a losing battle against the increasing number of enemy mobile suits. Back on Earth, Kira is alarmed when the Archangel receives news about the current situation of the Eternal. Realizing that Lacus is in dire need, Kira launches in the Strike Rouge (with an attached booster to enable it to reach space and its settings modified to those of the original Strike). Arriving on the scene, Kira is able to back up Waltfeld and disables a few ZAKUs and GOUFs, but the Strike Rouge is soon overpowered by the newer models and takes heavy damage; at this point, Waltfeld contacts Kira telling him to go to the Eternal and retrieve his new machine.

Inside the Eternal, Lacus presents Kira the Strike Freedom and he launches in it. Kira then proceeds to decimate 25 enemy mobile suits within 2 minutes, all while demonstrating Strike Freedom's Super DRAGOON System. After disabling the mobile suits, Kira disables the weapons and engines on the Nazca-class ships chasing the Eternal.

Operation Fury - ZAFT's Invasion of Orb[]

ZAFT intelligence tracks down Blue Cosmos leader Lord Djibril to Orb, where he is being sheltered by the Seirans. Carpentaria forces gather for an invasion along with the Minerva. Chairman Gilbert Durandal issues an ultimatum demanding that Orb hands over Djibril before he escapes and unites with the remaining Logos benefactors at the Moon via Orb's mass driver. Yuna responds to the ultimatum with an obvious lie: Djibril is not being protected by Orb and that the presence of ZAFT's fleet is an insult to the nation's sovereignty. The blatant disregard of the ultimatum enrages ZAFT leaders and Durandal authorizes the invasion of Orb to begin.

The ZAFT fleet deploys forces in the air and underwater and quickly disposes the hastily deployed Orb fleet, as the Seirans had chosen not to mobilize the military even in the face of invasion from ZAFT forces, while ground forces begin drilling into Onogoro. On the Archangel, Cagalli is enraged by Seiran's announcement, foreseeing it as a clear signal for Orb to burn once more (especially since the civilian population has not been made aware of the situation) and receives her father's will, the ORB-01 Akatsuki Gundam, from Morgenröete chief engineer Erica Simmons and Ledonir.

After launching in the Oowashi Akatsuki with the forces from the Takemikazuchi, Yuna, who is fighting a losing battle against the ZAFT forces, is removed from command after Cagalli tricks him into acknowledging her as Orb's Chief Representative (Yuna previously labelled her an impostor) and then ordering his arrest on charge of treason. After assuming command of the Orb fleet, she successfully rallies her remaining forces to push back ZAFT on all fronts. However, she then confronts and is almost defeated by Shinn in the Destiny. At the same time, Kira, arrived in the Strike Freedom and saves Cagalli from the Destiny's beam boomerangs. Kira then engages Shinn. Lacus, who is piloting the ∞ Justice Gundam, arrives on the Archangel to deliver the mobile suit to Athrun. While the Archangel engages the Minerva, Cagalli heads to Orb's military headquarters. With neither pilot gaining an upper hand, Shinn and Kira's battle ends when Rey orders Shinn to retreat as Destiny is running low on power.

Athrun, after talking to Lacus and overcoming some initial reluctance, launches in the ∞ Justice to aid Kira and confront Shinn despite still being injured. Djibril begins his escape from Orb as three ZGMF-XX09T DOM Troopers, part of the Clyne Faction, arrived to join in the battle. At Orb's National Military Defense HQ, an enraged Cagalli demands that a battered Yuna tell her where Djibril is, and he admits he has no idea where Dijbril is now. A resupplied Destiny launches again, this time with Rey in the Legend. The pair prove to be more than a match for the Strike Freedom. As Shinn was about to launch the finishing blow, he was interrupted by Athrun, who rams the ∞ Justice's shield into the Destiny. While Strike Freedom fights Legend, Athrun attempts to reason with Shinn while fighting the Destiny. The Archangel then submerges underwater and turns the tide of the battle by destroying several submarines and surface ships, including Operation Fury's flagship St. Helens.

Amidst the confusion, Djibril heads for space in the Seirans' private space shuttle. The Orb fleet sends Murasames in pursuit, while Gladys orders Lunamaria to sortie and shoot down the shuttle in the Force Impulse. When the shuttle manages to escape into space despite Orb and ZAFT sending units after it, Gladys orders a retreat for the ZAFT forces. As the Destiny and Legend withdrew, Athrun passes out from his injuries, leading to the ∞ Justice free-falling, but is rescued by Kira and rushed back to the Archangel for emergency medical treatment.

In the aftermath of the battle, Cagalli addresses the world regarding the ZAFT invasion, but she is interrupted by a broadcast by Meer (again posing as Lacus), to turn public opinion against Orb for sheltering Djibril. In response, the real Lacus interrupts Meer's broadcast, introducing herself as the real Lacus and declares that she still supports the Archangel. She goes on to say that she does not approve the actions of Chairman Durandal nor Djibril, and that people in the world should stop blaming everyone but themselves for the war.

Battle of Requiem Station Gounod - The Requiem Tragedy[]

After Djibril's escape, he makes it to the new Daedalus Lunar Base on the dark side of the Moon and authorizes the activation of the Requiem superweapon. The weapon consists of an enormous beam cannon site on the moon and several orbital relay stations built from abandoned colonies that use oversized Geschmeidig Panzer systems to alter the course of the beam. Fired from the fixed moon site, the beam is then bent at each relay point, and eventually guided to the primary target. Djibril orders it to be fired at PLANT's capital, Aprilius One, in order to eliminate PLANT's Supreme Council and Durandal, not knowing that he was elsewhere. However, due to combat in the vicinity of the Gounod relay station between the EA escort fleet and the ZAFT's Joule Team, the beam goes slightly out of alignment and instead hits Januarius 1 to 4, with Januarius 4 colliding into December 7 and 8, killing over a million of Coordinators. The Joule Team destroys the Guonod in retaliation, while also realizing that there are still multiple relay stations remaining that Requiem could use to hit the PLANTs.

At around the same time, from the notes on Durandal's Destiny Plan, the crew of the Archangel discover what his true intention is: Durandal plans to implement a new world order where every human is given the role for which they are best genetically suited for at birth, to fulfill his ideal of perfect genetic determinism. So the crew of the Archangel decides to head to space in order to stop Durandal's plan from succeeding.

Battle of Daedalus[]

While Djibril waits for Requiem to be recharged for another attempt at destroying Aprilius One, Durandal orders the ZAFT Lunar Fleet to attack the relay stations in retaliation for Requiem attack, ZAFT forces (including the Joule Team) attacked furiously but were at a stalemate with the defending EA forces. The Minerva, along with the Destiny and the Legend, launch a surprise attack on Daedalus as a diversionary tactic to allow Lunamaria's ZGMF-X56S/γ Blast Impulse Gundam to infiltrate the base and access Requiem's firing chamber through a connecting service tunnel.

At the Fourier relay station, ZAFT managed to knock it out of position before Requiem is fully recharged, but Djibril orders that Requiem be fired anyway to wipe out the ZAFT forces there, and so he can use it as a cover to escape to the Arzachel Lunar Base in the Girty Lue.

However, Lunamaria succeeds in destroying the Requiem control center before it can fire, and along with Shinn's and Rey's machines, the Minerva destroys the base's defenses. Shinn destroys the base's hangar and command center, while Rey detects the launch of the Girty Lue and destroys it with the Legend's DRAGOON Pods, killing Djibril. The defending Earth Alliance forces then surrender.

The "Destiny Plan"[]

Assassination Attempt in Copernicus City[]

When the Archangel and its crew reaches space, it docks at Copernicus City on the moon, where Kira, Athrun, Lacus, and Meyrin go for a shopping trip. After being sighted, ZAFT bodyguards assigned to protecting Meer set a trap with the objective of eliminating Lacus. Using Meer's Haro, they send a note to Lacus and company indicating that Meer is about to be killed. Although they suspect it to be a trap, Athrun insists on trying to find her anyway, and Lacus states she wishes to see Meer as well. They meet with Meer, who becomes surprised and enraged to see the real Lacus. Meer tries to shoot Lacus with a pistol, but soon comes to her senses and accepts that she is not Lacus Clyne. Their meeting is short-lived, however, as Sarah, Meer's manager and primary bodyguard, attempts to assasinate Lacus by summoning a squad of ZAFT bodyguards to gun down the group. Athrun manages to kill the bodyguards, and although Sarah was injured, she manages to shoot at Lacus before Kira and Athrun can react, but Meer rushed in to shield Lacus and was shot instead. Kira and Athrun then fire at Sarah, killing her. Kira calls for Neo in the Oowashi Akatsuki to take them back to the Archangel so that Meer can receive medical treatment, but it was too late and Meer passes away.

Proclamation of the Destiny Plan[]

Almost immediately after the assassination attempt, Durandal appears in a global broadcast, taken aboard the ZAFT space mobile fortress Messiah. He addresses the Requiem attack on PLANT, and assures the world that Logos has been defeated. However, Durandal announces that there is one more enemy that humanity has to face, an enemy he addresses as "ignorance and ambition". He accuses Naturals of being too self-centered and conceited, essentially causing the suffering of others. He then announces his solution to this problem, and reveals the "Destiny Plan" - every human and Coordinator will be assigned the role that they are the most genetically suited to.

The nations of the world are shocked by the revelation, the only two governments expressing opinions were the Orb Union and the Kingdom of Scandinavia, who openly reject the Destiny Plan. Around the same time, Earth Alliance forces launched from the Arzachel lunar base (the reason for this was unknown, though a ZAFT official suggests it was because they were emboldened by Orb's open rejection of the plan). Atlantic Federation President Joseph Copeland, like other government leaders, attempted to contact Durandal. Durandal refuses to entertain them, as he believes that those who rejects the plan to be enemies of humanity. He then reveals that ZAFT has rebuilt Requiem and orders it to be fired at Arzachel lunar base, killing Copeland and wiping out most of the Alliance's fighting force and intends on using it on Orb next. Horrified, the Archangel crew, decided to stop the Destiny Plan.

The Orb Union launches its space fleet from Copernicus, consisting of the Archangel and three Izumo-class battleship, including the Kusanagi. The Eternal, Lacus's flagship, leads a number of Earth Alliance and ZAFT battleships loyal to the Three Ships Alliance, as well as Earth Alliance ships that survived the Requiem attack on Arzachel.

Attack on Requiem Station One[]

The Three Ships Alliance's plan against Requiem was two-fold: the Archangel and Eternal lay siege to one of the Requiem's relay station - Station One, while the Kusanagi and the other ships attack Requiem. As the Archangel and Eternal approached Station One, the Strike Freedom and ∞ Justice launched with their METEOR units as Lacus contacted the guarding ZAFT fleet, begging them on the integrity of their uniforms to let them destroy the relay station.

Though initially fazed, a ZAFT officer rallied the forces by claiming them to be the remnants of Logos. This slowed down the Archangel and Eternal enough to allow the Minerva and the ZAFT's lunar fleet to arrive. Yzak held back his ship, and joined Dearka Elsman's Blaze ZAKU Phantom in battle with a custom-colored GOUF Ignited. Lunamaria also entered the battle in the Force Impulse. However, her assault was stopped when her sister Meyrin called out to her from the Eternal, demanding to know why she is fighting the real Lacus, shocking Luna who was then attacked by the three DOM Troopers.

During the battle between the Archangel and Minerva, the former was unable to evade the latter's "Tannhäuser", less it strike the Eternal instead. In a surprising move, the Shirunai Akatsuki piloted by Neo, came between the two ships, blocking the shot with the Akatsuki's unique Yata-no-Kagami armor. Neo's memories as Mu La Flaga then returned. Surviving the attack, he destroyed the Tannhäuser, protecting the Archangel. As Yzak and Dearka, who are allies of the Three Ships Alliance, keeping watch, Athrun and Kira used their METEORs' beam swords to cleave Station One in half. As the Three Ships Alliance forces rejoin the remaining forces, the Minerva halted their battle to give chase.

In the mean time, the combined Three Ships Alliance/Orb fleet attacks Requiem's main cannon, with much less success. Although the three Izumo-class ships fire their "Lohengrin" at Requiem, they were unable to penetrate Requiem's positron reflectors. Without warning, ZAFT's mobile space fortress Messiah appeared from behind the moon and fires its Neo-GENESIS superweapon, resulting in the destruction of part of the combined fleet.

Battle of Messiah: Assault on Requiem[]

As the Three Ships Alliance/Orb Forces regrouped, Shinn and Rey launched in the Destiny and Legend from Messiah, both having been summoned there earlier during the siege on Station One. Kira and Athrun undocked from their METEORs and went to engage the two, Kira's Strike Freedom against Rey's Legend and Athrun's ∞ Justice against Shinn's Destiny. Meanwhile, ZAFT began to gain an advantage over the Three Ships Alliance/Orb fleet. Realizing the desperate situation, Kira ordered Athrun and the Archangel to deal with Requiem while he and the Eternal held off the others. Despite their reluctance, they agreed and went off to stop the superweapon. In response, Rey ordered Shinn to chase the Archangel and defeat Athrun once and for all. As Kira continued his fight with Rey, he found that somehow Rey keep reminding him of Rau Le Creuset. Later, Rey took the name of Rau, blaming Kira for how humanity has acted. Rey was shocked when Kira pointed out that he always had his own life and it never belonged to Rau. Kira then used this chance to fire Strike Freedom's Full Burst Mode, crippling the Legend.

Near Requiem, Athrun encounters Lunamaria and her Force Impulse. Lunamaria has conflicting feelings over everything and was unable to battle effectively. The ∞ Justice then swiftly defeated the Force Impulse by slicing off its right arm and leg, before Shinn arrived to help. Meanwhile, Mu in the Shiranui Akatsuki decided to attack the Requiem, and orders a squadron of Murasames to join him. As Shinn and Athrun fought, Athrun attempted to get through to Shinn. However, blinded by his rage and his loss of Mayu and Stella, Shinn refused to listen and continued his attacks. Lunamaria eventually came between the two, but Shinn suffered a psychotic break, forcing Athrun to push the Force Impulse aside and completely disables the Destiny. The Destiny crashed on the lunar surface, and Lunamaria worriedly went after Shinn.

The battle between the Archangel and Minerva reached its climax when Athrun entered the battle. Though the Minerva took out one of Archangel's "Gottfried" dual beam cannons, the Archangel was able to destroy Minerva's "Tristan" dual beam cannons before Athrun rams the ∞ Justice's Fatum-01 through the ship's engines, forcing an emergency crash landing on the Moon. Durandal attempted to use Neo-GENESIS to destroy the Three Ships Alliance/Orb fleets, only to take out more of the remaining Earth Alliance forces along with allied ZAFT forces due to Yzak's warning. With mere seconds left before Requiem fires again, the ∞ Justice and the Shiranui Akatsuki penetrated the positron reflectors and destroyed the Requiem at the cost of the ∞ Justice's Fatum-01. The explosion could be seen from the landing spot of the Destiny's wreckage, where Shinn finally broke down in Luna's arms because Orb wasn't hit.

Re-equipping the METEOR, Kira's Strike Freedom destroys the Messiah's positron reflector generators. With the fortress' defenses weakened, the Eternal launched a barrage of missiles, ravaging Messiah's surface and destroying Neo-GENESIS. As Kira entered the crippled base, he was soon joined by Athrun. Meanwhile, Gladys ordered the crew of Minerva to abandon ship and requested her executive officer Arthur Trine to watch over the crew as she leaves for Messiah. In Messiah, Kira confronted Durandal and they argued over Kira's uncertain future filled with the promise of an actual tomorrow and Durandal's predicted and premeditated ideal world. Rey, Gladys, and Athrun later arrive separately. Durandal was eventually shot by Rey, who was affected by Kira's words. As Messiah fell towards the Moon, Gladys and Rey opted to stay behind with a dying Durandal; Gladys also asked Kira to tell Murrue to go and visit her son some time. As Messiah crashes, killing the three, Lacus contacted the ZAFT ship Gondwana to request a ceasefire and the remaining ZAFT forces agreed, bringing an end to the hostilities.

Aftermath[]

Sometime in C.E. 74, PLANT and Orb Union signed a ceasefire agreement and started negotiating for an end to the war. The PLANT's Supreme Council later requested Lacus, who had acted as a mediator between the two nations, to return. At an unspecified time, Kira and Shinn met on Onogoro Island by chance and they mended fences. Later, Lacus became the PLANT Supreme Council Chairwoman, Kira joined ZAFT, while Athrun remained in the Orb Union.

A year later, Lacus left her position, and with the help of Kira and company, formed the new peace monitoring organization Compass to stop the growing conflict between ZAFT and remnants of Blue Cosmos which broke off the Earth Alliance after the existence of Logos. The actions of the recently established Kingdom of Foundation, who secretly intended to apply the Destiny Plan, then led to the Foundation Conflict.

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