Second Alliance-PLANT War

The Second Bloody Valentine War is the second major conflict in the Cosmic Era.

Background
Almost two years have passed since the Bloody Valentine War between the Earth Alliance and ZAFT ended with the Treaty of Junius Seven. The treaty placed restrictions on the numbers of mobile suits that could be maintained, and nuclear weapons N-Jammer and N-Jammer Canceller, as well as the Mirage Colloid were banned outright (for military use only).

ZAFT provided N-Jammer Cancellers to the Earth Alliance to solve its impending energy crisis, caused by the "April's Fool" attack on Earth, in which ZAFT buried N-Jammers deep underground to prevent any further nuclear attacks on PLANT, killing millions after people on Earth completely reliant on nuclear power found themselves without electricity. All political power and territories taken by the Earth Alliance from the neutral nation of the Orb Union was to be returned to the Orb government.

The Treaty of Junius Seven 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 faction Blue Cosmos, reorganized under the leadership of Lord Djibril, and continued to exercise influence over Earth's political elite.

Peace Treaty notwithstanding, both ZAFT and Earth Alliance continued to expand their military assets, including development of mobile suits units. Even if nuclear technologies were banned, some of it remained secretly on their development agendas.

Armory One Incident (October 2, C.E. 73)
With both ZAFT and Earth Alliance members building up their military powers, Orb Union representative Cagalli Yula Athha arranged a meeting with ZAFT chairman Gilbert Dullindal to discuss the need for power in the post-war era. Athrun Zala accompanied her as a bodyguard, under the alias "Alex Dino". The meeting took place at ZAFT's Armory One, which was currently preparing for the launch ceremony of the first post-war battleship, the Minerva.

While Cagalli met with Dullindal, Earth Alliance pilots Sting Oakley, Stellar Loussier, and Auel Neider infiltrated the base, commandeered ZAFT's newest Gundam-type mobile suits, ZGMF-X24S Chaos, ZGMF-X31S Abyss, and ZGMF-X88S Gaia, and heavily damaged the installation.

Various ZAFT mobile suit units engaged battle, including ZGMF-1000 ZAKU Warriors, ZGMF-X56S Impulse, piloted by Shinn Asuka, and the crew of the Minerva. The stolen units succesfully escaped the colony, and were picked up by the Mirage Colloid-cloaked Earth Alliance battleship Girty Lue, stationed 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 Junius Seven Colony Drop.

Junius Seven Colony Drop - Operation Break The World
The theft of the three Gundams was immediately set aside when movement was detected from Junius Seven, which was supposed to be in a stable orbit. A rogue ZAFT force that supported the late Patrick Zala planted engines all over the colony's remains, sending it on a collision course with Earth.

A ZAFT squadron under the command of Yzak Joule was dispatched to break up the colony, and was soon reinforced by the approaching Minerva's mobile suits. They were engaged in close combat battle by the rogue squadron, who easily outperformed the members of the Joule team, and operations to break Junius Seven in pieces were compromised. The Girty Lue also arrived on the scene, launched the stolen mobile suit units and engaged the Minerva.

The Minerva forces successfully broke Junius Seven in two pieces just as it began entering the upper atmosphere. During atmospheric descend the Girty Lue and the survivors of the Joule team withdrew, but Minerva continued to pursue the debris, breaking it into smaller fragments with her main Tannhäuser cannon. The destruction was insufficient, and the pieces crashed to Earth, destroying Athens, Philadelphia, Quebec City, part of the Great Wall of China, Shanghai, Rome and numerous other locations, while pieces that hit the sea caused massive tidal waves. The most severe damage occurred near the equator.

An alliance of the Junk Guild, the Serpent Tail and Rondo Mina Sahaku tried to use GENESIS Alpha to push away the remains of Junius Seven but due to the intervention of the RGX-00 Testament the operation failed.

In the aftermath of the disaster, ZAFT immediately sent humanitarian aid to Earth. Lord Djibril, leader of the Blue Cosmos, divulged photographic evidence showing rogue ZAFT units executing the drop, and started uprising the public opinion into blaming coordinators for the disaster. He also used his position within the secret society Logos in order to influence or even directly command the leaders of the Atlantic Alliance to start a war against PLANT.

Second Bloody Valentine War
Fueled by public opinion, manipulated by Blue Cosmos, the president of the Atlantic Federation sent a list of demands to PLANT's 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.

Dullindal 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 Bloody Valentine War.

Battle of Aprilius One
The Earth Alliance main force launched its battleships and mobile suits against the main PLANT defense, which managed to repel the attack. Meanwhile, a separate ambush team moved to attack Aprilius One, the location of the Supreme Council. The team launched a squadron of new-model GAT-04 Windam units carrying nuclear warheads, but fortunately a scout unit located them in time. Knowing that the Earth Alliance might try to use nukes, a Nazca-class vessel was equipped with a Neutron Stampeder. When the device was activated, it sent out high frequency radiation that detonated all the nuclear weapons in the Earth's ambush fleet, which was completely destroyed. Having failed in their mission to destroy PLANT, 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. Dullindal, knowing of the possible escalation of the conflict, used the help of a Lacus Clyne look-alike idol Meer Campbell to calm the people.

Dullindal assigned ZGMF-X23S Saviour to Athrun, now reenlisted in ZAFT. Athrun was also appointed as FAITH, a special forces unit reporting directly to Dullindal, effectively given permission to use his power as his conscience dictated. He departed for Earth, to join the Minerva and comunicate to Talia Gladys her own appointment to FAITH.

Operation Spear of Twilight
Following the 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 around their bases.

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

The majority faction of Orb's governing body, led by Prime Minister Unato Ema Saran and his son Jona Roma Saran, supported an alliance. Cagalli, Orb representative, remained fiercely opposed. The council feared the Atlantic Federation' 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 forced into accepting the alliance.

Orb declared it would sign the International Safety Assurance Treaty.

Minerva's Ambush at Orb
Orb council planned to give the Minerva to The Earth Alliance as a gift of good faith. The Minerva was still at dock 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 beam deflector. An Orb fleet was deployed on the border to prevent 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 technology and Shinn Asuka's SEED factor were instrumental in the battle. The damaged Minerva headed for the ZAFT Carpentaria base in Australia.

Attempted Assassination of Lacus Clyne
After the First Bloody Valentine War, the main figures of the Clyne Faction lived secretly in an orphanage in Orb, hiding both the Archangel ship and the stolen ZGMF-X10A Freedom unit.

A unknown mobile suit task force attempted to assassinate Lacus Clyne at the orphanage, but was incapacitated by Freedom. All the pilots killed themselves after being defeated, and evidence suggested the units used were manufactured by ZAFT.

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. Before leaving, Kira Yamato kidnapped Cagalli, during her wedding with Jona Roma Saran.

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 due to a Mobile Armor equipped with a positron deflector. The destruction of the fortification, which had become known as the "Lohengrin Gate", resulted in the liberation of the city which had been occupied and oppressed by EA forces. The locals quickly repaid the brutality and cruelty that had been shown to them and executed numerous captured EA soldiers and officers.

Battle of Dardanelles
On route to the Gibraltar ZAFT base, the Minerva departed from the ZAFT base in the Black Sea, but was intercepted by a Earth Alliance fleet in the Dardanelles strait. Despite Orb Union's historical non-aggression policy, in the light of the new alliance Orb couldn't refuse orders from the Earth Alliance, and a massive fleet comprised of several carriers and MVF-M11C Murasame mobile suit units engaged the Minerva.

Soon after, as the Minerva was to fire its main cannon on the leading Orb ship, her Tannhäuser cannon was destroyed by ZGMF-X10A Freedom, piloted by Kira Yamato, killing several crewmen from the Minerva in the process. The intervention of the Archangel stalled the battle, and Cagalli tried to stop Orb officials to attack the ZAFT forces. Her pledge failed as Jona Saran claimed her an impostor and ordered the leading Orb ship to fire on Cagalli's mobile suit 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 it's three remaining mobilesuits, a ZGMF-1000 Zaku Warrior, a ZGMF-1001 Zaku Phantom, and the prototype ZGMF-X2000 GOUF Ignited, to back up the ZGMF-X56S Impulse and ZGMF-X23S Saviour which had already sortied to defend the ship. The fighting was fierce, the Archangel and the Freedom tried to continue to carefully launch attacks designed to deter combat mobile suits and disable aggressive units. However Kira Yamato's intervention provoked the death of Heine Westenfluss, whose mobile suit he disabled, allowing Stellar Loussier to destroy Heine's Gouf Ignited while Heine was distracted with Freedom and moved into the way of Gaia's attack. 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.

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 Colonel Todaka and Jona Roma Saran. The Archangel, with Kira's Freedom and Cagalli's Strike Rouge, unsuccessfully tried again to stop the Orb forces by disabling various units. The battle group under the command of Neo Lorrnoke also participated to the battle, closing the Minerva in a pincher move.

The Chaos and Abyss units engaged Shinn's Impulse and Athrun's Saviour. Left with only two mobile suits as cover, the Minerva was attacked by the entire Orb mobile units force, consisting of several attack groups of Murasame units. The attack was repelled, but the Minerva took very heavy damage, including both the catapults, part of the mobile suit hangar, the main deck and most of the upper armor. While defending the ship, Rey Za Burrel's ZAKU Phantom was damaged and Lunamaria's ZAKU Warrior was destroyed. Athrun's Saviour was destroyed by Kira's Freedom; all three pilots survived.

While Kira was engaged with Athrun, Shinn managed to destroy the Abyss, killing its pilot Auel Neider. In supporting the Minerva, Shinn then decimated the Orb mobile unit force, and after that he directly engaged the Orb fleet, sinking several ships. The aircraft carrier Takemikazuchi launched a frontal attack on the Minerva, but under fire by Impulse and Minerva's main cannons, it exploded and sank before reaching the Minerva. Colonel Todaka valiantly chose to sink 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.

Battle of Berlin
After Lord Djibril assigned the massive mobile suit GFAS-X1 Destroy to Neo Lorrnoke, the designated 'Extended' human pilot Stellar Loussier effectively used it to destroy several cities in Western Eurasia.

The Destroy was intercepted by ZAFT forces over the city of Berlin. ZAFT units were no match for the Destroy's massive energy weapons and anti-beam shields, and Berlin was heavily damaged. Soon after, both the Archangel and the ZAFT ship Minerva, with their complement of mobile suits, arrived on the scene and joined the battle against the Destroy.

Kira Yamato in the ZGMF-X10A Freedom engaged the Destroy, along with Cagalli Yula Athha in the Strike Rouge, three Orb Murasames, and both Minerva and the Archangel. When the Destroy's shield was disabled by Shinn, Neo Lorrnoke communicated that the pilot was Stellar. Shinn's feelings stopped him from finishing the Destroy. During this time, the Freedom approached and Stellar reacted, and Kira stabbed the Destroy on the chest, mortally wounding Stellar in the process.

During the battle, the pilot of the ZGMF-X24S Chaos chose to retreat, but sustained heavy damage by the trio of Murasames. As his mobilesuit plumetted towards the ground, it was cut in half by the Murasame team leader Ikeya. The cockpit was not penetrated, but the fragments of the mobilesuit were in volatile condition and detonated. Oakley was initially believed dead but managed to survive and returned the the Earth Alliance, after which he was transferred and stationed at Heaven's Base.

Kira Yamato, on a hunch, disabled Neo Lorrnoke's Windam, and allowed Neo himself to be captured by the Archangel. Stellar died in Shinn's arms.

At the end of the battle, Berlin was nearly destroyed, which led to more tension between the Atlantic and Eurasian Federations and the break down of the original Earth Alliance. Leaving the Atlantic Federation to effectively fight ZAFT on their own.

Dullindal Exposes LOGOS to the World
After the battle, at a news conference that is broadcast across the PLANTS and Earth, Chairman Dullindal tells people that there is an information gap, so he shows video footage of the war and gives a speech: he says that the Alliance's excuse was to liberate Western Eurasia from ZAFT, but asks if destruction was liberation (It should be noted that the video footage showing the Battle of Berlin and the destruction of the GFAS-X1 Destroy the Freedom has been removed, giving Impulse the credit for defeating the Destroy). Meer Campbell joins the conference and says that the war was set up by ZAFT radical extremists. Dullindal 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 Alliance's shadowy military-industrial benefactors had been manipulating world events and was the cause of major wars, including the Bloody Valentine Wars. He explains that even the Alliance's Blue Cosmos rulers are just a tool of Logos. When he shows the photos and names of all Logos members (including Djibril who unsuccessfully ordered the broadcast to be cut off), Dullindal said that Logos wanted people to fight for their profit and vows that ZAFT will destroy Logos in order to bring peace between the Earth and the PLANTS. The speech greatly strengthen Earth's support for ZAFT and weakened civilian support for the Alliance. The ZAFT campaign to destroy Logos and Blue Cosmos has begun. The crew of the Archangel after seeing the broadcast decide to head to Orb fearing it might be attacked due to the fact that Orb is affiliated with the Earth Alliance. Several Earth Alliance Naval fleets defect and station themselves at Gibraltar.

Operation 'Angel Down'
Operation 'Angel Down' commenced when an AWACs Zaft mobile suit picked up the Archangel on its sensors, as the Archangel was on its way to Orb. ZAFT sends the Compton, one of their newer models of land battleships, and it's mobile suits, a compliment of BuCUE's and BABI's begin to attack the Archangel. The Archangel and Freedom try to escape.

The goal of the operation was to sink the Archangel and destroy the Freedom, as the ZAFT HQ claims that they have only caused confusion during the war. The Minerva was ordered to take part in the battle. If the Archangel made it to the sea and managed to dive, the battle would be over.

When Minerva arrives, the Impulse engages the Freedom. The Compton stops its attacks. Impulse repeatedly blocks Freedom from defending the Archangel or running away. The Impulse's pilot, Shinn Asuka, had been studying the moves of the Freedom with help of Rey Za Burrel, and uses preplanned tactics to battle the Freedom, allowing him to easily outperform Kira.

During the battle, Talia Gladys, Captain of the Minerva, tells the Archangel to throw down their weapons and they will be spared. Captain Ramius of Archangel politely refuses, claiming that they only wish to return to Orb. At this point the land battleship resumes its attack, claiming that Gladys is too soft.

At the climax of the battle, Archangel begins to dive into the sea, while the Minerva fires its Tannhauser Positron Blaster Cannon. Once the positron beam hits the ocean, it generates a massive explosion, which heavily damages the submerged Archangel, but does not directly destroy the ship. Captain Ramius ordered one of the main engines to be jettisoned and detonated as a ruse to buy time to escape. It was later confirmed by ZAFT's underwater search team that the Archangel had escaped intact.

At the same time, the Impulse makes creative use of its many Silhouette packs, and by taking advantage of Kira Yamato's fighting style (which primarily involves disabling the enemy MS weapons/cameras), manages to impale Freedom with an anti-ship sword. Kira Yamato disabled his nuclear reactor, which, as a side effect, shut down his unit's phase shift armor, allowing his unit to be torn apart when it was hit by the shockwaves of the nearby explosion. Shinn Asuka believed that his attack had completely obliterated the Freedom and therefore avenged Stellar's death. In truth the shielded cockpit in the upper torso survived intact, and Kira Yamato was later rescued by his sister, Cagalli Yula Athha.

Athrun's Defection
Athrun was angry that ZAFT had to destroy the Archangel as Kira Yamato was his friend and because he believes that their motives were to reduce the bloodshed, but Gilbert Dullindal thinks that they have only caused confusion throughout the war. After he unveils the ZGMF-X42S Destiny and the ZGMF-X666S Legend, Dullindal and Rey Za Burrel have a meeting and decide that Athrun's emotional attachement to the Archangel prevents him from being 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 MPs sent to arrest him.

Athrun then escapes into Meyrin Hawke's room after Meer refuses to go with him. After Meyrin sets off a false alarm to distract the soldiers, the two escape in a GOUF mobile suit. However, they were found by Za Burrel, 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 Dullindal and Rey, Rey convinces Shinn that Athrun is unstable and the GOUF was destroyed by Shinn's Anti-Ship Sword. However, Athrun and Meyrin were recovered by Ledonir Kisaka, the former Kusanagi captain from the first war, and the two are transferred to the Archangel's infirmary in Orb.

Battle of Iceland - Operation: Ragnarök
ZAFT and 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 being attacked. Before the time limit expires the ZAFT/EA forces are aswered by a sudden barrage of rockets. Also a great number of mobile suits, some new mobile armors as well as five GFAS-X1 Destroy units (one unit piloted by former ZGMF-X24S Chaos pilot Sting Oakley) are deployed against the joined ZAFT/EA forces. Because of this, many of the anti-LOGOS EA ships and mobile suits are destroyed, especially by the GFAS-X1 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 orbit. However LOGOS is well prepared for this and order the activation of the powerful Nibelung weapon, which sends out a massive energy burst (similar to the GENESIS superweapon), destroying all units coming from above and crippling the already weakened forces.

The Minerva finally launches the Destiny, Legend and Impulse (piloted by former Gunner ZAKU Warrior pilot Lunamaria Hawke) 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 Forbidden Blue units Shinn and Rey attack the five Destroy units. Shinn then orders Lunamaria to switch to the Sword Silhouette and give one sword to Rey, and three pilots then set to work eliminating the Destroys with Destiny's Arondight and Impulse's Excalibur anti-ship swords. In the destruction of the five Destroy units, pilot Sting Oakley is killed when Shinn drives an Anti-Ship Sword into Sting's cockpit. In the meantime, ZAFT forces gain the upper hand when they able to successfully penetrate the base. Lord Djibril, knowing that Heaven's Base is all but lost, abandons the other LOGOS members and flees in a submarine towards Orb.

The Eternal's Plight
While the battle of Heaven's Base rages on Earth, in space another set of events are taking place. DeCosta journeys to the Mendel space colony to retrieve evidence about Dullindal's plans (how the Clyne Faction learned of this is unknown). While DeCosta is examining a laboratory, he discovers a research notebook which he takes and returns to the Eternal (but he is followed by a scout GINN). Aboard the Eternal, Lacus and Waltfield examine the journal and ponder the meaning of the "Destiny Plan" outlined in it; however, they are interrupted by an alarm signaling that they have been discovered by ZAFT forces.

Lacus immediately orders the Eternal to launch so they can try to deliver the ZGMF-X20A Strike Freedom and ZGMF-X19A Infinite Justice to the Archangel at all costs; As they get near Earth, they are ambushed by two more ZAFT ships and multiple squads of ZAKU's and GOUF's; knowing that the situation is grim, Waltfield decides to launch in the stolen ZGMF-X88S Gaia. Back on Earth, Kira is alarmed when the Archangel receives news about the Eternal's current condition; realizing that Lacus is in dire need, Kira launches in the Strike Rouge (with an attached booster to enable it to reach space). Arriving on the scene, Kira is able to disable a few ZAKU's and GOUF's, but the Strike Rouge is soon overwhelmed and heavily damaged by the superior units; at this point, Waltfield contacts Kira telling him to dock with the Eternal and retrieve his new unit.

After docking with the Eternal Kira launches in the Strike Freedom and proceeds to disable the attacking mobile suits. After disabling the mobile suits, Kira disables the ZAFT ships chasing the Eternal.

ZAFT Invasion of Orb - Operation: Fury
ZAFT intelligence tracks down Blue Cosmos leader Lord Djibril to Orb, where he is being sheltered by the Sarans. Carpentaria forces gather for an invasion along with the Minerva. Chairman Gilbert Dullindal issues an ultimatum demanding the capture of Djibril before he escapes and unites with the remaining LOGOS benefactors at the Moon via Orb's Mass Driver. Jona Roma Saran responds with an obvious lie: Djibril is not being protected by Orb. The disregard of the ultimatum enrages ZAFT leaders and Dullindal 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 Sarans had chosen not to mobilize the military even in face of the threat from ZAFT forces, while ground forces begin drilling into Onogoro. In the Archangel, Cagalli Yula Athha is enraged by Saran's announcement, foreseeing it as a clear signal for ORB to burn once more (expecially as the civilian population has not been made aware of the attack)and receives the 'legacy' of her father, ORB-01 Akatsuki, from Morganroete Chief Engineer Erica Simmons and Ledonir Kisaka.

After launching in the Akatsuki, Cagalli removes Jona from command after tricking him into acknowledging her as Orb's military commander and then ordering his arrest on the account of treason. However, she is then confronted and almost killed by Shinn Asuka in the Destiny. Kira Yamato returns from space piloting the Strike Freedom and engages Shinn (who's shocked that the Freedom's pilot is alive). Lacus Clyne, who returned with Kira, delivers the Infinite Justice unit to Athrun Zala on the Archangel. While Archangel engages the Minerva, Cagalli retreats to the Orb military headquarters. With neither gaining an upper hand, Shinn and Kira's battle ends when Rey Za Burrel orders Shinn to retreat to recharge the Destiny's battery.

Athrun, after talking to Lacus and overcoming some initial reluctance, launches in the Infinite Justice to aid Kira and confront Shinn. Djibril begins his escape from Orb as the three DOM Trooper units of the rogue Clyne Faction arrive to join the battle. At Orb's National Military Defence HQ, Cagalli demands that Jona reveal Djibril's location, who admits he has no idea. A resupplied Destiny launches again, this time with Rey in the Legend. The pair prove to be a match for the Strike Freedom, as the Strike Freedom is knocked into a point of vulnerability. Shinn is about to use this chance for a crushing blow but is interrupted by Athrun. While the Freedom engages the Legend, Athrun attempts to reason with Shinn (who receives a second shock upon realizing Athrun is alive) and fights Destiny. The Archangel then submerges under water and turns the tide of the battle after destroying several submarines and surface ships of the ZAFT marine forces, including Operation: Fury's flagship St. Helens.

In the confusion of the battle, Djibril manages to launch in a shuttle. The Orb fleet sends Murasames in pursuit while Talia Gladys orders Lunamaria Hawke to shoot down the shuttle in the Force Impulse. When the shuttle escapes to orbit, Gladys orders a retreat and ZAFT forces disengage from battle. Athrun collapses as the Orb forces withdraw and is rushed back to the Archangel by Kira for emergency medical treatment.

While there was no official confirmation if Dijibril had indeed escaped, Dullindal agreed with Talia's decision. Post-battle, Cagalli addresses the world regarding the ZAFT invasion, but she is interrupted by a broadcast by Meer Campbell (again posing as Lacus Clyne). In response, the real Lacus Clyne interrupts Meer's broadcast, introduces herself as the real Lacus and declares that she is still on the Archangel's side. She goes on to say that she does not approve the actions of Chairman Dullindal nor of Lord Djibril, and that people in the world should stop blaming everyone but themselves for the war.

REQUIEM Attack on Aprillus One
After Lord Djibril escapes, he makes it to the new Daedalus lunar base of the EA, and authorizes the activation of the Requiem superweapon. It is composed of an enormous cannon site on the moon as well as several orbital relay stations containing extra-large Geschmeidig Panzer units. Launched from the fixed moon site, the beam is bent at each relay, and eventually guided to the primary target. Djibril orders it to be fired at the PLANT capital, Aprilius One. However, due to combat at one of the relay sites between the EA escort fleet and the Joule squad of ZAFT, the beam goes out of alignment and instead hits Januarius 1 to 4, with Januarius 4 colliding into December 7 and 8, killing an estimated of 900,000 Coordinators. The Joule team destroys one relay in anger, but after recharging there are still multiple relay stations Requiem could use again to fire at the PLANTs.

Around the same time, from the notes on Chairman Dullindal's DESTINY Plan, the crew of Archangel discover what his true intention is: That he will implement a new world order where every human is given the role for which they are best genetically suited at birth, to fulfill his ideal of perfect genetic determinism. So the crew of the Archangel decide to head up into space in order to stop Dullindal's plan from succeeding.

Battle of Daedalus EA Base
When Chairman Dullindal orders the ZAFT Moon Fleet in attacks on the relay stations in retaliation for the Requiem attack, the ZAFT forces (including the Joule Squad) attacked furiously but were at a stalemate with the defending EA forces. The Minerva stages a surprise attack on the Daedalus lunar base in order to destroy the Requiem's main cannon with their Legend and Destiny units. The EAF deploys its last three GFAS-X1 Destroy units and several mobile armors to defend the base. ZGMF-X56S Impulse is assigned to infiltrate the base and destroy the control center of Requiem. The team manages to defeat all three Destroy units and obliterates all the other MAs. Lord Djibril's attempt to escape on the Girty Lue towards the Arzachel lunar base is detected by Rey Za Burrel and the ship is destroyed by the Legend's DRAGOONs, thus killing the last member of LOGOS and Blue Cosmos leader.

Assassination Attempt in Copernicus City
When the Archangel and its crew reaches space, it docks at the free city of Copernicus on the moon, where Kira Yamato, Athrun Zala, Lacus Clyne, and Meyrin Hawke go for a shopping trip to the city. After being sighted, ZAFT bodyguards assigned to protecting Meer Campbell set a trap with the objective of eliminating Lacus Clyne. 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. After trying to shoot Lacus with a pistol, however, Meer comes to her senses and comes to accept that she is not Lacus Clyne. Their meeting is short-lived, however, as Sara, leader of the ZAFT bodyguards, attempts to eliminate Lacus by summoning a squad of ZAFT bodyguards to gun down the group. Athrun manages to defeat the bodyguards, but Sara managed to survive and tries to shoot Lacus. Meer, in an attempt to shield Lacus from harm, is shot instead. Kira and Athrun then fire back at Sara, effectively killing her. Kira calls for Neo Lorrnoke in the ORB-01 Akatsuki to take them back to the Archangel for Meer to receive medical treatment, but Meer dies before she can be moved.

Dullindal Reveals the Destiny Plan
Almost immediately after the assassination attempt in Copernicus City, Chairman Gilbert Dullindal appears in a global broadcast, taken aboard the ZAFT space mobile fortress Messiah. From the Messiah, he address the Requiem attack on PLANT, and assures the world that LOGOS has been defeated. However, he 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. Thus, he then announces that he has the solution to this problem, and reveals the Destiny Plan. PLANT then uses the Requiem superweapon that they captured at the Daedalus Base and use it against Arzachel Base, destroying it and killing the President of the Atlantic Federation. After this, an unknown number of ZAFT and Earth Alliance vessels join up with the Eternal, while the Archangel leads a fleet of Izumo-class battleships, including the Kusanagi. Both ships' fleets head towards the same destination, Requiem itself, while the Eternal and Archangel head for the Requiem's first relay point.

Attack of Requiem and its First Relay Station
As Archangel and Eternal approach Requiem's first relay station, they encounter ZAFT's defense forces guarding the station. Lacus Clyne attempted to convince the defending ZAFT forces to back off but failed. As a result, a hard battle broke out between the forces of the Clyne Faction and ZAFT. During the battle, Yzak Joule and Dearka Elsman switched sides and protected the Strike Freedom and Infinite Justice while they use their METEOR units to destroy Requiem's first relay station. In the meantime, the combined ORB, EA and ZAFT rebel fleet attacked Requiem's main cannon. Although many Orb Izumo class ships fired their Lohengrin positron cannons on the Requiem, they failed to do any damage to it. This was because the gateway of the Requiem was protected by positron reflectors. Without warning, ZAFT's Mobile Fortress Messiah appeared from behind the moon and fired its Neo-GENESIS superweapon, resulting in the destruction of part of the combined fleet.

Battle of Messiah
The Archangel and Eternal regrouped with the Orb fleet and began engaging the ZAFT forces defending the Messiah space fortress and the Requiem. However, with Requiem's second station moving closer to Orb, Kira Yamato, pilot of ZGMF-X20A Strike Freedom, told the Archangel and Athrun Zala, pilot of ZGMF-X19A Infinite Justice, to break through the Requiem's shield and destroy it. On the way, Kira was engaged by the ZGMF-X666S Legend, piloted by Rey Za Burrel, who blamed Kira for his flawed existence. However, Rey was shaken by Kira's reasoning as to his own life, and had Legend nearly destroyed. In the meantime, Athrun was attacked by Lunamaria Hawke piloting the ZGMF-X56S Impulse. Athrun easily disabled Impulse, but was attacked by the ZGMF-X42S Destiny, piloted by Shinn Asuka. Lunamaria tried to put herself between the two to stop the fight, but when Shinn came close to destroying Impulse by accident, Athrun saved Lunamaria in time by disabling Destiny, sending it crashing to the Moon.

The Minerva, which had engaged the Archangel, was severely damaged when the Archangel disabled the majority of its weaponry, and Athrun disabled its engines. The Minerva crash-landed on the Moon, disabled, but the crew survived. Meanwhile, ZAFT Chairman Gilbert Dullindal authorized the firing of the Requiem and ordered the Neo-GENESIS superweapon to fire on the Orb fleet. However, as he informed his forces of the Neo-GENESIS firing, Yzak Joule notified the Eternal to move the fleet out of the way. Thus, the Neo-GENESIS missed its target, destroying mostly ZAFT vessels, as well as some Earth Alliance battleships that had followed the Clyne Faction. As the REQUIEM prepares to fire, the Infinite Justice and the ORB-01 Akatsuki, piloted by Neo Lorrnoke, managed to penetrate the Requiem's positron deflector and destroy the Requiem.

The Strike Freedom and the Eternal managed to heavily damage the Messiah. Kira infiltrated the Messiah in order to assassinate Dullindal. Rey and Talia Gladys, captain of the Minerva, also infiltrated the Messiah to seek Dullindal. As Kira and Dullindal come to a standoff, Rey, completely shaken by Kira's words, shoots Dullindal in an act of frustration. Both Rey and Gladys choose to stay on board the Messiah, and they die along with Dullindal as it explodes. Kira was able to escape the Messiah before it crashed on the Moon.

In the "Final Plus" episode, Athrun also entered the Messiah and was responsible for identifying Gladys, instead of Kira alone as shown in the "original" (i.e. in FINAL-PHASE). He escaped in the Infinite Justice, along with Kira in the Strike Freedom, and later rescued Shinn and Lunamaria from the surface of the moon.