Star Fox faces their toughest challenge yet once they learn that Andrew has taken over Andross' work and plans on destroying the Lylat System. Now the squadron must team up with other mercenary pilots from across the universe in order to put a stop to him, all while trying to defeat a dangerous enemy squadron known as the Fireflies.

When a new enemy appears to threaten the peace in Lore, Brihart and his friends soon realize that their lives are in danger and that they must stop this villain by any means necessary.