Corneria,fourth planet of the Lylat System. The evil Andross turned this once thriving system into a wasteland of near extinction. General Pepper of the Cornerian Army was successful in exiling this maniacal scientist to the barren,deserted planet Venom. Five Years Later,General Pepper noticed a strange activity coming from Venom. James McCloud,Pigma Dengar,& Peppy Hare of the Star Fox Team were sent to investigate. Upon their arrival,Pigma betrayed the team and James & Peppy were captured by Andross. James sacrificed himself to allow Peppy to escape.
A few Years later,Fox goes to the Academy where he met Falco Lombardi & Slippy Toad. Andross' Army invaded Corneria. Fox managed to stop them with Falco & Slippy's help. After this,The Star Fox Team is reborn. They are joined by Fay,Katt,Miyu,& Pepper's son,Bill. They are even joined by Peppy.
Andross learns about this and has his Nephew Andrew Oikonny join the Star Wolf Team,Wolf O'Donnell,Leon Powalski,& Pigma. At Corneria,General Pepper sends the Star Fox Team to recover their stolen army base from the Venomian Invader Fighters. By the time they got here,The Star Wolf Team attacks them. After Andrew's Wolfen Wing gets damaged,Grangar aids the Star Wolf Team with his Mech. Rob 64,the team's robotic operator,detected the bomb that the Star Wolf planted inside the base. Fox manage to stop it while Falco & Slippy took down the Mech,killing Grengar.
The Star Fox Team must go to Venom to stop Andross. While there,They were confronted again by the Star Wolf Team. After Pigma gets shot down,Wolf & Leon retreat. Fox confronts Andross and starts firing at him several times. After his outer layering of his head gets destroyed,Andross reveals his true form: an enormous brain with bulging eyes. Fox manage to blast Andross,causing him to burst into quickly escapes with the help of James' Spirit as Andross exploded. Back at the Great Fox,General Pepper declared the Star Fox Team as heroes.
Mid-Credits: Pigma survives the crash and calls out,but no reply.