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.

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.

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.

When transport cruisers mysteriously disappear en-route to rebuild Pluto Alpha Base, X-Bomber is assigned to defend the next convoy of ships.

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”.

X-Bomber’s new mission to seek out the Skull is put on hold when the Imperial Alliance renews their assault on Earth.

Trapped in a black hole and rapidly losing power, the crew of X-Bomber desperately fight a losing battle against Commander Makara’s forces.

X-Bomber seeks shelter on the planet Aloria, unaware of its deadly secret.

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.

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.

Shiro, Hercules and Lee investigate a distress call from a devastated planet of war, however their new enemy is not far behind.

Enraged by Captain Custer’s latest attempt to destroy X-Bomber from within, Shiro faces his former mentor in a dual to the death.

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.

Lamia is summoned once again by the Skull, but wary of another Imperial Alliance trap, Dr. Benn refuses to let her go.

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.

With X-Bomber badly damaged and the crew unconscious, Lamia fights to avoid capture by hordes of Imperial soldiers boarding the ship.

While the crew struggles to repair the stranded X-Bomber, Lamia learns of her heritage and the secret of F-Zero-One.

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.

As time rapidly runs out for Lamia, the crew of X-Bomber and their new ally Captain Halley try desperately to trace her whereabouts.

Bloody Mary employs vicious new measures to destroy Lamia, with fatal consequences for one of the X-Bomber crew.

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.

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.

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.

Despite the Imperial Master’s attempts to stop them, X-Bomber continues on its journey back to Earth.

At the dawn of the year 3000, the crew of X-Bomber face the final battle against the Imperial Master, and learn the power of F-Zero-One.