After saving Equestria from a local and very dangerous threat, Fox McCloud settled down, married Krystal and they got a son together: Marcus. Everything perilous about his work has stopped, just going on escort missions and liveries from one side to another of the Lylat System.

Twilight Sparkle is now the sole ruler of Equestria, doing a pretty good job during the last ten years of her peaceful reign. All along the way, she was helped by Spike who was her ambassador. Everything was going just fine until a space armada made its appearance in Equis' sky. The suddenness of their arrival and their technological advance proved to be too much for the locals, even with the strongest pony to history at their side.

Yet, not all hope is lost. The only chance for the planet for be freed from the invaders rests on the shoulders of one group: The Star Fox Team.