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During the Cosmic Era, Earth and space territories have been divided up by Naturals and Coordinators.
Naturals
Earth Alliance
The Earth Alliance is a Naturals based militia organization. This organization is composed of many nations working together to fight against ZAFT forces. The Earth Alliance was formerly known as OMNI (Oppose Military Neutralize Invasion).
Blue Cosmos
The Blue Cosmos is run by Naturals. They are anti-Coordinators and they have very strong ideals opposing Coordinators. Blue Cosmos is basically composed of Naturals who despise all Coordinators. It is lead by Muruta Azreal, who is extremely selfish. Their general idea is to eliminate all Coordinators for "a pure and blue world."
Logos
Not much is known about this organization, except that they seem to strongly support the Blue Cosmos. As explained by ZAFT's Chairman Dullindal, they are the ones who promote war between Naturals and Coordinators because they would profit from war munitions.
Coordinators
ZAFT
Zodiac Alliance of Freedom Treaty. ZAFT is a Coordinator based organization. It is Coordinators' defense and offense against Naturals. In Gundam SEED, it was lead by Chairman Zala, whose goal was to eliminate all Naturals. After his death, Gilbert Dullindal was elected ZAFT's chairman. His ideals are different than Patrick Zala's.
FAITH
FAITH is an elite ZAFT organization composed of only the top guns in ZAFT's militia. Members of FAITH are allowed to do as they please in battle without the captain's permission. Only those who demonstrate excellence in ZAFT are promoted to FAITH.
Others
Orb
The Orb Union is composed of many islands on Earth as well as some space colonies. Orb is a neutral nation lead by Uzumi Nara Athha in CE 71. During that time, Orb was threatened by the Atlantic Federation to disband its neutral policy. Orb refused and held onto their ideals, even though it was difficult be neutral during a war like this. Orb's main ideal is that
it will not attack another country nor allow any other country to attack them. This is how Orb works to remain a neutral nation.
Clyne Faction
Clyne Faction was established shortly after the Clyne family were marked as traitors to ZAFT. It is run by Lacus Clyne and is an organization to promote peace among both kinds. It was first introduced when Lacus communicated with the world by radio. Soon after, Lacus and her crew successfully take over the Eternal. From there, they would be able to stop the war.