This are some of the independent factions that arose in C.E.
1.2 Three Ships Alliance
The Clyne Faction started as the collection of PLANT politicians loyal to the ideals of Siegel Clyne, leader of the PLANT moderate faction. However, as the political situation in the PLANTs took a dark turn, the group switched to being an underground rebel faction comprised of normal civilians and ZAFT soldiers, spawned as a result of Patrick Zala's extremist genocidal politics towards the Naturals. The Clyne Faction was initially commanded by former PLANT Chairman Siegel Clyne, but after his assassination, his daughter, Lacus Clyne, took over. Another prominent figure was Andrew Waltfeld, a much-decorated ZAFT commander.
Their first major actions were the theft of the ZGMF-X10A Freedom and soon after the hijacking of the newest ZAFT capital ship, Eternal, which was coincidentally assigned under the command of Andrew Waltfeld by ZAFT. Even though Zala is in charge of ZAFT and uses it to try and crush the Clyne Faction, the ease in which the Clyne Faction managed to steal the Freedom and the swift hijacking of the Eternal later on highlights the fact that the Clyne Faction likely has a considerable number of supporters within ZAFT as well.
II. Three Ships Alliance
The Three Ships Alliance was formed near the end of the Bloody Valentine War as a force dedicated to ending the war. It consisted of the members of the Clyne Faction who had stolen the ZAFT support vessel Eternal, survivors from the Earth Alliance invasion of Orb aboard the Orb battleship Kusanagi, and the crew of the Earth Alliance assault ship Archangel. The Three Ships Alliance takes up residence in an abandoned space colony for a little over two months, and then sets out to prevent the Earth Alliance and PLANT from annihilating each other. The Three Ships Alliance was instrumental in preventing an Earth Alliance nuclear assault on the PLANT colonies, and in preventing PLANT from using the GENESIS Superweapon from irradiating the Earth.
After the Bloody Valentine War, the Three Ships Alliance (composed of the Clyne Faction, moderate elements of the Atlantic Federation, and remnants of the Orb Military) was changed into a covert moderate military and political organization once again operating under the Clyne Faction name. This new faction received aid from the independent intelligence group Terminal, strengthened in numbers and technology thanks to defecting Earth Alliance and ZAFT officers and appears to have thoroughly infiltrated the military command structure of every major faction. It is also implied that Terminal has very well-placed intelligence sources as information about current events such as the Minerva's departure time and the Destroy's rampage across Western Eurasia were received and sent to the proper people within a very short amount of time. And thanks to backing from the Orb Union, Terminal became one of the world's main political and military organizations, although its influence can be called discreet, even subversive. Spawned for the same reasons as the Three Ships Alliance, to achieve and maintain peace and stability between Coordinators and Naturals; the Clyne Faction was lead by Lacus Clyne on the political side and Kira Yamato on the military end.
Despite considerable military expansion by ZAFT and the Atlantic Federation (the strongest member of the Earth Alliance), Terminal too developed advanced military hardware with its large industrial base, which includes a secret underwater base and a mobile suit factory hidden in an asteroid. The ZGMF-X20A Strike Freedom, ZGMF-X19A Infinite Justice, and ZGMF-XX09T DOM Trooper, all of which were made by Terminal from technology originally developed by ZAFT, are generally on-par or even superior to their ZAFT and Earth Alliance counterparts. Towards the end of the Second Bloody Valentine War, Terminal and Terminal-allied forces consisted of one Archangel Class, one Eternal Class, three Izumo Class, two to three Agamemmnon Class, at least four Nelson Class, at least two Drake Class, at least two Nazca Class and at least two Laurasia Class warships. Their mobile suit forces were spearheaded by the Strike Freedom, Infinite Justice, Akatsuki, Gaia, and three DOM Troopers. The main body of their mobile suits comprised of dozens of Murasame, Dagger-L and Windam mobile suits.
After stealing the Eternal, the Clyne Faction was joined by Orb's remaining military forces aboard 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 Ships 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 Ships Alliance and secretly headquartered on the abandoned Mendel colony. Their purpose was to put an end to the war which was rapidly growing beyond all control, 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) now believed that genocide was the only way to achieve victory.
This small fleet succeeded in saving the PLANT colonies from the Earth Alliance's initial nuclear assault, and Earth from the ZAFT's superweapon GENESIS. The Bloody Valentine War came to an end with the help of the Three Ships Alliance, which managed to counteract the threats on the civilian population and put an end to the war, in September, Cosmic Era 71.
After the war, the TSA went again underground. The Eternal and Archangel were hidden, and most of the crews moved to Orb, under pseudonyms. After the Second Bloody Valentine War, new factions of Orb's government manipulated it into joining the Earth Alliance, and the Clyne Faction members in Orb took the Archangel and Freedom (both hidden in secret facilities in Orb) and fled. While the Eternal had a quiet role in the war to date, the Archangel actively tried to intervene in EA-ZAFT battles that involved the Orb fleet, with Cagalli Yula Athha trying to appeal to the Orb soldiers to leave the battle. Though the Archangel was joined by a large number of Orb officers and pilots from the sunken Orb carrier Takemikazuchi, ultimately their attempts failed and their interventionist policies have created tension between both the Earth Alliance and ZAFT, and they have undoubtedly caused chaos on the battlefield.
Seeing that the Clyne Faction would not be able to achieve their objectives alone, Lacus Clyne relocated to the newly created Terminal organization and its covert orbital factory to oversee its operations. Under her supervision, Terminal constructed new advanced mobile suits - the ZGMF-X19A Infinite Justice, and ZGMF-X20A Strike Freedom, as well as the obtaining of the ZGMF-X88S Gaia, and the obtaining and completion of the three prototype ZGMF-XX09T DOM Trooper units.
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 chairman Gilbert Durandal, fearing the Clyne Faction's potential interference in his plans, declared them to be an enemy of ZAFT and justifying their decision by citing the group's numerous interferences in ZAFT battles. 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 Morgenroete.
ZAFT discovered the presence of the Terminal Factory (which also hid the Eternal) and sent a force of three Nazca class battleships to attack it. With the ZGMF-X88S Gaia the only functional mobile suit (and piloted by Andrew Waltfeld), the factory was heavily out-numbered so Eternal in an attempt to draw the ZAFT forces away from it, and prepared to drop the newly-completed ZGMF-X19A Infinite Justice and ZGMF-X20A Strike Freedom towards Orb should the ship be lost. Fortunately, Kira Yamato arrived in the MBF-02 Strike Rouge via an orbital booster and, after taking possession of the ZGMF-X20A Strike Freedom, defeated all of the pursuing ZAFT forces.
A short time later, during ZAFT's assault on Orb (codenamed Operation Fury), the Archangel participated in the defense of Orb. Meanwhile, Kira Yamato in the ZGMF-X20A Strike Freedom departed the Eternal and made an unassisted re-entry to help in the battle, while towing the ZGMF-X19A Infinite Justice (which was being "ridden" by Lacus Clyne) on order to deliver it to Athrun Zala. The three ZGMF-XX09T DOM Trooper units also participated, arriving from the Eternal via an orbital drop pod. Together with the Archangel, the Eternal's mobile suits successfully defended Orb. After Cagalli regained control over Orb, the crew of the Archangel were formally included into the Orb military. After Durandal exposes his Destiny Plan, The Orb space fleet (including the Archangel, the Kusanagi, and two of the Kusanagi's sister ships), the Eternal, and Terminal-supporting ships from both ZAFT and the Earth Alliance, along with the Kusanagi's sister ships, set out to oppose Durandal's destiny plan.
The group once again had the distinction of helping to end the war, when the ORB-01 Akatsuki and ZGMF-X19A Infinite Justice destroyed the Requiem superweapon, and the ZGMF-X20A Strike Freedom destroyed the Messiah mobile space fortress.