After saving the Lylat System in Lylat Wars/Starfox 64, the Starfox Team have been out of jobs, out of luck and out of money, in times of peace there is no need for warriors.

Far away on the planet of Sauria, a new evil stirs in the form of one General Scales, dictator and ruler of Dinosaur planet.
We are introduced to our foxy heroine Krystal, who respond's to a distress call from the planets surface, encountering the General and aiming to help the planet, she triggers an event that will yet again call the heroic Starfox team back into action!