The Three Ships Alliance was created during the Bloody Valentine War to end this war.
Clyne Faction
The Clyne Faction started as a underground rebellion faction of ZAFT soldiers, spawned as a result of Patrick Zala's extremist genocidal politics towards the Naturals. The Clyne Faction was commanded by Lacus Clyne, daughter of Siegel Clyne, leader of the moderate faction in the PLANT Council. Another prominent figure was Andrew Waltfeld, a pluridecorated ZAFT commander.
Their first major actions were the theft of the ZGMF-X10A Freedom and soon after the hijacking of the newest ZAFT battleship, the Eternal, assigned by ZAFT to Andrew Waltfield.
Terminal
After the Bloody Valentine War, the Three-Ship-Alliance (composed of the Clyne Faction, moderate elements of the Atlantic Federation, and remnants of the Orb Military) was changed into a moderate military and political organization called Terminal. Terminal was strengthened in numbers and technology thanks to defecting Earth Alliance and ZAFT officers; and thanks to backing from the Orb Union, Terminal became one of the world's main political and military organizations. Spawned for the same reasons as the Tree-Ship-Alliance, to achieve and maintain peace and stability between Coordinators and Naturals; the figurehead of Terminal was Lacus Clyne.
Despite considerable military expansions by ZAFT and the Atlantic Federation (strongest member of the Earth Alliance); Terminal too developed advanced military hardware. The ZGMF-X20A Strike Freedom, ZGMF-X19A Infinite Justice, and DOM Troopers are generally on-par or more advanced than their ZAFT and Earth Alliance counterparts. Towards the end of the Break The World War, Terminal consisted of one Archangel Class, one Eternal Class, three Izumo Class, two to three Agamemmnon Class, at least four Nelson Class, at least two Nazca Class and at least two Laurasia Class assault carriers. Their mobile suit forces were spearheaded by the Strike Freedom, Infinite Justice, Gaia Gundam, Akatsuki, three DOM Troopers; and body comprised of dozens of Murasame and Dagger-L mobile suits.
History
Shortly thereafter they were joined by the remaining space forces of Orb, in the Izumo-class battleship Kusanagi, and the defected Earth Alliance assault ship Archangel. Both the newest ZAFT mobile suit units, the stolen Freedom and ZGMF-X09A Justice, had already joined the Archangel, but were soon transferred to the Eternal, which was equipped with the METEOR System, specifically built for those two units. However, thanks to the assistance of Reverend Malchio, the Three Ship Alliance was able to make contact with several peace-seeking groups in Orb and the EA, and the rest of the Clyne Faction headquartered in the PLANTs. Also, the group received a tender ship, the ReHOME, complements of Reverend Malchio and the Junk Guild.
The new rogue faction became known as the Three Ship Alliance and secretly headquartered on the abandoned Mendel colony. Their purpose was to put an end to the war before it got out of hand, as both the Earth Alliance (Now under the control of Blue Cosmos) and ZAFT (Under the command of Patrick Zala and his radical extremist faction) were willing to commit genocide to the other group.
This small fleet succeeded in saving the PLANTs from the nuclear missiles fired by the Blue Cosmos-dominated Alliance fleet, and Earth from the ZAFT's superweapon GENESIS. The Bloody Valentine War came to an end with the help of the Three Ship Alliance, which managed to counteract the threats on the civilian population and put and end to the war, in September, Cosmic Era 71.
After the war, the TSA went again underground, their ships were hidden. Most of the crew moved to Orb, under pseudonyms. When the Second Bloody Valentine War began, these individuals took the Archangel and Freedom and fled Orb, which had joined the Earth Alliance and became involved in the conflict. While the Eternal has had a quiet role in the war to date, the Archangel has actively tried intervened to reduce the amount of bloodshed and destruction caused in various battles but failed. Their interventionist policies have created tension with both the Earth Alliance and ZAFT, and they have undoubtably caused chaos in the battlefields.
At a later stage in the war, the Archangel and ZAFT's battleship Minerva joined forces and fought together against the Earth Alliance's prototype mobile fortress, the GFAS-X1 Destroy. However, ZAFT's command structure declared them to be an enemy of ZAFT. The Minerva later participated in Operation "Angel Down", with the objective of destroying the Archangel. During this conflict, Minerva fired its positron cannon on the fleeing Archangel, and Impulse was able to defeat Freedom with the clever tactics of its pilot Shinn Asuka using Kira Yamato's unwillingness to kill, as the Freedom's pilot. However the Archangel managed to survive despite being badly damaged while the Freedom was destroyed. Kira Yamato, was saved by Cagalli in the MBF-02 Strike Rouge and the Archangel then continues en route to Orb. The Archangel finally arrives at Orb, where it is repaired in a secret base by Morgenröete.
It also appears that the Clyne Faction was secretly working on new mobile suits on the Eternal if there would be a new war. These suits are the ZGMF-X19A Infinite Justice, ZGMF-X20A Strike Freedom and three units of the mass production model ZGMF-XX09T DOM Trooper. These units later, together with the Archangel, defended Orb when ZAFT attacked the country. After Cagalli regained control over Orb, the crew of the Archangel were formally included into the Orb military. After Dullindal exposes his Destiny Plan ships from both ZAFT and the Earth Alliance join the Eternal in a combined fleet and the Archangel leading a fleet of Izumo class ships including the Kusanagi.
The group once again had the distinction of helping to end the war, when it's ORB-01 Akatsuki and ZGMF-X19A Infinite Justice units destroyed the Requiem laser cannon, and it's ZGMF-X20A Strike Freedom unit destroyed the Messiah mobile space fortress.