It is C.E. 71. The Earth Alliance forces have just won a bloodbath of a victory against the ZAFT forces at the Alaska base, despite suffering near total losses themselves. Unbeknownst to many in the Alliance military, the inner circle of the Alliance deliberately destroyed Alaska base in order to wipe out the ZAFT forces at all costs. So, the inner circle has gotten away with one of the most devious acts in the history of the world.

Not knowing the truth of what happened at Alaska, our friends have gone their separate ways. Lt. Mwu la Flaga is now a pilot instructor in California. Lt. Murrue Ramius and Ens. Natarle Badgiruel continue to serve aboard the Archangel. Kira Yamato, is also still aboard the Archangel as its chief mobile suit pilot, but he now pilots the Freedom Gundam instead of the Strike Gundam. Kira's friend Athrun Zala, after realizing what ZAFT really wanted in this war, has joined Kira aboard the ship. Dearka Elsman, Athrun's colleague in ZAFT, is also aboard the Archangel, though as a POW.

But soon, very soon, all of their lives will come together once again. The inner circle has conceived a plan to not only cripple the ZAFT forces on Earth, but to eliminate their main enemies in the Alliance military. Now all is in shadows, but one of the most titanic struggles in the history of the world is about to take place. Should our heroes fail their objectives, they will pay the ultimate price with their lives.