Gundam Seed Destiny begins two years after the first Gundam Seed ended. Many believe that peace will come about with the radicals of both sides dead. The chairman of ZAFT is Gilbert Durandel who seems to be focused on peace. As with the first series, the leader of the Earth Alliance is unclear and fairly irrelevant, but there are some key Earth Alliance characters who pilot mobile suits.
ZAFT: Headed by Chairman Gilbert Durandel, ZAFT seems to be at a stable stage with a much stronger military. They crank out new mobile suits including a set of new Gundams. A key addition to the ZAFT militia are the Zakus, mobile suits that commonly resemble mobile suits of other Gundam series. They feature the one eyeball, the antenna on the head, and the spiked shields. Dearka and Yzak from the first series are still with ZAFT from the original Le Creuset team that also featured Athrun Zala.
Earth Alliance: The Earth Alliance begins the war largely with demands that are illogical and obviously meant to provoke war. As with the first, special forces invade to steal mobile suits, but this time, it's the Alliance stealing the ZAFT suits. This force is made up of three young pilots, all with strange colored hair who are later found to be drug-injected super soldiers. The Alliance is largely controlled by the Blue Cosmos/Logos group which is anti-Coordinator. They also maintain their policies that there cannot be any neutral countries and ORB is forced to ally with the Alliance. The most intriguing part is that a soldier similar to Le Creuset and wearing a similar mask but sounding like Mu La Flaga is seen at the beginning.
ORB: The Orb Union is now headed by Cagalli Yula Atha, but she is subject to the opinions of the Council of Elders who aid her and also by her arranged fiancee Yuna Roma Seyran. Kira and Lacus are also residents of ZAFT, but would seem to be ther only with the knowledge of a few people. The Freedom and the Archangel are revealed to be here as well as the majority of the Archangel's crew.
The main plotline revolves around the second Cosmic War. The Earth Alliance seems to be the initiator of the conflict, but it is later discovered that Logos is behind it. Chairman Durandel declares war on Logos only to find that a third player, the Archangel, is also involved. The story line focuses much more on the ZAFT aspect in regard to Athrun Zala, the former ZAFT soldier and son of former leader Patrick Zala. He is originally with ORB, but goes on a visit to ZAFT to investigate the Plant's actions and is convinced by Durandel to join ZAFT again. Throughout the war, he is confused as to who he should be fighting, especially when ZAFT is ordered to attack ORB and then to declare the Archangel and the Freedom as enemies.