Desperate to cut off the ties of his new and hollow life, Fox McCloud makes a blind jump into unknown space. Thinking the planet is devoid of sentient beings, Fox settles down and starts his new life of solitude. Meanwhile, a young Cerinian warrior Krystal and her wayward tribe are fleeing their destroyed village while a savage horde hunts them down.

Star Fox is all but disbanded in the wake of the Anglars. After years alone, Fox faces the stagnation which quickly resumes its stranglehold on both Lylat and his life. Forces stir beneath the surface of the Cornerian Federation which may promise freedom or threaten destruction - as the distant stars themselves whisper possibilities of warmth and life... or brutal cleansing fires.

Fox learns that Krystal is engaged with Panther, and becomes extremely distraught. However, he meets another woman who picks his hopes back up. Who will Fox end up with? Krystal or the other woman?