The year is Universal Century 0133. Ten years have past since the armed resistance of the aristocratic fraction, the Crossbone Vanguard, was subdued. Tobia Aronnax is an exchange student onboard the spaceship Smashion to Jupiter, but during a surprised attack by a group of space pirates who call themselves the Crossbone Vanguard, he finds out that there were actually hidden agendas among those in the Smashion and in Jupiter itself.

After being saved by a member of the pirates named Kincaid Nau, he was taken aboard the pirate ship, the Mother Vanguard, and was convinced by its captain, Berah Ronah, to join them. The pirate group's true identity was revealed to be a guerilla group resisting the secret fraction within Jupiter, the Jupiter Empire, which intends to conquer Earth. Now Tobia must pilot one of the three powerful Crossbone Gundam to help this new Crossbone Vanguard in their quest to oppose the Jupiter Empire's plans.