It is the year 2201. The Yamato has returned from the devastating battle with Emperor Zordar and the Comet Empire. Sanada, Aihara, and Shima are released from the hospital, and go to pay their respects to the fallen crew members at Okita's memorial. They meet Tokugawa's son Tasuke, who says that he will be joining the crew once he graduates from cadet school. The next day at his graduation, he ends up capsizing a boat full of new cadets because they are all too busy staring at the Yamato to watch where they are going. After some problems during launch due to the new engine crew hitting the wrong switches and stalling the ship, the Yamato departs on what should be a simple training mission.

A remake of episodes 12-13 of the TV version.

The Persona Century Corporation has purchased nearly every parcel of land on earth. Dissension is not tolerated within the corporation's borders and those who oppose Persona are dealt with swiftly. Of those few places not yet under Persona's control is the free town of Kabuki-cho, also known as "The Dark Side of Tokyo". Within the town, under the leadership of a woman named Mai, is a small resistance group called Messiah. Into this world steps a man who takes the sobriquet of Kabuki-cho: Darkside. Sealed up in another dimension eighteen years ago by Persona Century, Darkside now returns to aid Messiah using his unique mystic power of renewal.

A freak accident unleashes a demonic spirit within researcher John Stalker - transforming him into Saldo, a mythical cyber-beast fueled by hate and evil.