During a contest to win rights to salvage and perform shows in the Sea of Lorelei, Rick Aller rescues Rosa the Second (Rosa II) when her mercenary crew turn on her. With her mobile suit damage, and his own small mobile armor damaged as well, they hide inside a sunken submarine that has been resting on the ocean floor since the 7th Space War. While investigating the ship they discover a black GX-9900 Gundam X and decide to use the mobile suit to escape in. But when they open the cockpit they discover the pilot of the mobile suit is still inside of it and in a state of suspended animation. Awakening him they make... their escape from the ship and defeat the mercenaries that turned on Rosa II.

Introducing himself as Kai, the pilot of the black Gundam X displays unusual abilities that lead the crew of the Vulture ship to speculate that he is a Newtype. Mirage Weiss, the captain of the Vulture ship Mirage, decides to take Kai to a Newtype Lab after Kai starts to suffer a mental break down. When they arrive to find the Newtype Lab destroyed, Kai leaves the ship and uncovers the powerful Gundam Belphagor, and battles Rick as he pilots the black Gundam X. Rick is rescued by Rosa II when she arrives in her GS-9900 G-Falcon, and together they flee as Kai destroys the Mirage with a single shot from the Gundam Belphagor's weapons. Joining up with a quirky female mechanic named Mana, a survivor of the destruction of Fort Severn by Carris Nautilus in the anime, they repaint and repair the Gundam X. Together they start a pursuit of Kai, who has now joined a mysterious organization that have rebuilt D.O.M.E., the true purpose of why and what the group intends are unknown.