Remnants, a name whispered in the darkest corners of Lylat, very little is known about them, but General Pepper has gotten wind of the scope of their plans and five months after the Aparoid Conflict, he hires Star Fox to look into the group. Remnants, Star Fox, Corneria, Wolf's Ruffians, Caroso's Legion, when the dust settles and calm rules again, only one will be left standing.

One year has passed since the downfall of the aparoids, but the Lylat System is far from being at peace. Andross' rebel forces are stronger than ever, led by an enemy that Fox and his team thought was killed during the aparoid invasion. While Fox and his friends fight corruption spreading from the inside, a new threat emerges claiming war and revenge against the Lylat System.

After nearly 5 months of the Star Fox team disbanding, Fox McCloud is tired of being a slum and tired of being alone so he sets out on a quest to help defeat the Anglers and to reform his team and love life.

One week after the Aparoid War, Fox and his team are given a new mission. A mission that Team Star Fox may not be able to complete on their own...

With the new addition of Krystal to the team, Fox couldn't be happier as they find their affections for one another growing. But the rest of the team questions Fox's decision and Krystal's capabilities as an uneasy tension begins to form, especially with the recently returned Falco.