Learning of the Imperial Master’s plan to assault the Earth, the crew of X-Bomber begins a hurried journey back home. However a defeated Bloody Mary and Kozlo are not far behind and will do anything to regain their honor.
As war rages on the planet Callinean, the crew of Dai-X face their toughest battle yet – defending the Royal palace against the latest Alliance weapon.
Shiro meets a face from the past when X-Bomber lands on the planet Callinean. In the meantime, the Imperial Alliance prepare for an onslaught against the peace loving inhabitants of the planet.
Returning to the Alliance Base, Bloody Mary and Kozlo are promoted and get drunk celebrating. Meanwhile Halley continues to try and contact Lamia, but the extreme cold of her prison is getting to her and her thoughts are becoming weaker.
Lamia begins exhibiting supernatural powers and tries to convince the skeptical crew of X-Bomber that the Imperial Alliance has launched an all-out assault against them.
Facing the dawn of a New Year in deep space, Shiro, Hercules and Lee reminisce over the events of the war with the Imperial Alliance and the fate of Captain Custer.
Responding to a summons from the Skull, the crew of X-Bomber find themselves trapped by a ruthless new Alliance Commander – one with a disconcertingly familiar voice.
Bloody Mary and Kozlo are summoned back to their home world by the Imperial Master. Charged with their continuing failure to defeat X-Bomber and capture F-Zero-One, they face trial and execution.
Shiro, Hercules and Lee search Pluto for the lost Captain Carter – their former tutor at the academy. Meanwhile, Lamia receives a summons from a mysterious sailing ship, “The Skull”.
The Imperial Alliance lay siege to Earth Defense Forces, demanding the handover of the “F-Zero-One”. The crew of X-Bomber battle against time to repair their ship before Star Fleet Command is destroyed.
Unable to gain contact with the crash-landed X-Bomber, Lamia attempts to reach the ship and help the crew, but comes under heavy attack from Imperial Alliance fighters.
2999: a gigantic Imperial Alliance battlecruiser wipes out the EDF's Pluto Alpha Base and heads for Earth. General Kyle orders X-Bomber to intercept it but the craft is only 90% complete and not up to the task. Badly damaged in the ensuing battle, it crashes on the Moon.