Two years after the war in CE 73, conflicts between ZAFT and the Earth heat up again. ZAFT's, which now lead by Gilbert Durandal, new top pilot is the young Shin Asuka. Shin's eyes are full of sorrow as his family was killed in Orb during the war. Meanwhile, Athrun is torn between protecting Cagalli in Orb and doing something about the war. When the one who joined ZAFT, Shin, and the one who left ZAFT, Athrun, the story begins...