Part I Shogo Yahagi lives in what appears to be 1980s metropolitan Japan. He meets Yui Takanaka and discovers her roommates are his friends Mai Yumekano and Tomomi Murashita. Shogo's old friend Shinji Nakagawa shows him a military prototype Garland motorcycle (labeled "Bahamut") that can reach over of 300 km/h. He barely escapes as Shinji is killed by unknown agents. Shogo uses a public video phone to call Eve Tokimatsuri, a popular singer and TV host, during her show to expose the Garland to the public. The show's broadcast is cut off while Shogo shows Eve the bike (now painted red by a mechanic friend) and explains its capability. He escapes in another chase by agents and soon discovers it can also transform into a mecha. Shogo helps Tomomi make an action film centered around the mysterious bike and has Yui hide the Garland at night. While looking for film locales, Shogo finds a secret entrance to a hidden, abandoned city and battles with some of the advanced fighters he encounters, most importantly with a military big shot named B.D. After B.D. is nearly defeated, he informs Shogo about that Bahamut is a supercomputer that controls the events in this world, and that they are actually living on a spaceship, and that the real time is actually 500 years in the future. The military were developing new weapons underground to avoid Bahamut's detection, and that they have cleared "Level 6", Shogo shows mercy and leaves. He then sneaks inside Eve's recording studio, and finds out that she is actually a computer simulated idol. In his anger at the state of the world, he nearly rapes Yui, but she supports and understands him anyway, and they have a romantic night. He confides in her everything he's learned about the world and watches martial law unfold on the city. As the military clears "Level 7" of Eve's protection, B.D kills the Brass, manipulates the Prime Minister, and obtains financial support from the wealthy, notably Mai's father. Agents kill Tomomi and steal her master tapes, and a grief-stricken Mai returns to live with her father. Eve contacts Shogo through the Garland to ask him to help reactivate her reveals that the human race destroyed Earth, that there were actually 2 ships that left earth successfully and that Bahamut simulates the era of the 1980s because it was the most peaceful and full of love. Shogo goes back to the underground city, and battles with the military, but is defeated by B.D., who returns Shogo's mercy by sending him back up to surface. Badly wounded, Shogo deserts the broken Garland and apparently walks back to Yui's place. English Dub, Episode 1 of 4.

Part III - Day of Liberation Eve takes Eiji outside Eden to the ruins of Megazone to check on Bahamut and explains its control of Megazone and guidance back to Earth. They see Eden's outside machinery stretching out further to maintain the city. Eve activates Bahamut to run diagnostics on Eden, which reports status as normal. Eve wonders why Shogo did not wake her and asks Bahamut what happened to him. Bahamut directs her to the last remaining file on him in the next room, which contains the original Garland (from Part II) and a disk. As Eve and Eiji return to Eden, Sion prepares to take over Orange from its leaders who only want to crush C•X. In the battle, Bud is brainwashed and fights for them but is killed in the process, despite Eiji's attempts to save him. They reach Bishop Won Dai, who they now know to be a Megazone survivor, to stop Project Heaven, which was planned to launch Eden into space to save Earth from humanity again. As the city starts to rumble in the execution of Project Heaven, Eiji shows Won Dai the disk, and he recognizes it and snaps out of his trance, realizing he has been connected to the system for too long. From his last words it is hinted that Bishop Won Dai actually turns out to be Shogo, though how he ended up in the system after Part II remains unknown. As he dies while Eiji attends to him, Eve takes the Bishop's place to stop Project Heaven as the program is within her. She kisses Eiji (and "Shogo") goodbye through the glass shield that now surrounds her and brings the city back down, opening it back to nature. The city core, now controlled by Eve, launches into the sky, leaving the rest of the city on Earth. Eve tells Eiji that she will pilot the core to the Moon to destroy ADAM as well, thus freeing humanity from all of its artificial computer overlords. After watching Eve rise into the sky, Eiji returns to the streets to find Ryo waiting for him and the fighting over. English Dub, Episode 4 of 4.