In F-Zero U every playable pilot has their own story campaign. Compared to F-Zero GX's Story Mode, the player is able to complete more types of missions rather than just racing. Captain Falcon's story mode focuses on both his bounty hunting, and tracking down his arch-nemesis Black Shadow.
The story mode begins with a panning shot of what appears to be a mysterious corporation. The scene then extends to where an unknown figure is watching Captain Falcon taking down minions. This scene ends and begins the story mode.
- If the player completes chapter two, they will then gain access to Lily Flyer's story mode.
- If the player completes chapter one, they will then gain access to Blood Falcon's story mode.