Two years after the war between the Earth Alliance and ZAFT conflicts between the two nations heat up again. Shin Asuka the new main character'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. With new Mobile Suits being developed by ZAFT and the abduction of three new Mobiles by three Earth Alliance Pilots the new story begins.