As with nearly all the other 10000 Gundam shows, the premise for Gundam Seed involves the conflict between the earth dwellers and the space inhabitants, who live in giant space stations called colonies or satellites. At the beginning of the series we learn tension has been rising for some time between the two sides. Partially caused by economic reasons and also to the fact most of the space colonists are genetically enhanced (Coordinators) so a lot of normal people (Naturals) despise them and vice versa. This conflict erupts into an all out war after the Earth Alliance annihilates a peaceful farming colony in an event remembered as "Bloody Valentine". A year later, the war is still going on and this is where our story starts.

We are first introduced to a group of teens living on Heliopolis, a resource satellite belonging to a neutral nation, Orb. Everything is going great for the kids until Heliopolis is suddenly attacked by the alliance of space colonists (ZAFT) who are after 5 new mobile suits the Earth Alliance has secretly been manufacturing there. ZAFT is successful in capturing 4 of them, but a twisted turn of events finds one of the children, Kira Yamato, behind the controls of the 5th mobile suit. Because of being a coordinator, Kira easily adapts to piloting the suit and teams up with the Earth Alliance forces. Together along with his other school friends, they become the crew of Archangel, a giant legged spaceship, and set out on a mission to deliver the mobile suit to Alaska.