The Lylat System now lies in the hand's of Syxx, who now controls a force mightier than himself. Krystal has only one last chance to stop him but after Corneria's fate is forever changed, she realizes, Syxx will stop at nothing to extinguish them all.

She is a member of Starwolf, but feels Fox's "accidental" death was her fault. Now Fox walks the path of darkness as Syxx and becomes everything he vowed to destroy and he hates. Only Krystal can make him see again. But can she? How far has Fox gone?

shortly after the events of SFA, the team must live in the civilian world on Corneria for the next year waiting for repairs. During that time, Fox Reunites with Miyu. They along with Krystal then enter a love triangle, Fox then must choose who he loves.