The game is set within an alternate timeline from other Dodonpachi games, with all characters from previous games abandoned. In the past, the Element Doll Electronics Laboratory was designing the ultimate Element Doll to assist the human species, dubbed "Project Haruuara." The first units produced were Extra Z-001 "Hina" and Extra Z-002 "Saya." Though they lived as twin sisters and were taught the importance of closeness with humans, they were trained as enemies in combat. When Hina decided that the ultimate answer to humanity's problems was to eliminate the human person, she went berserk. The project was immediately shut down and both Hina and Saya were deactivated. Prior to the beginning of the game, Hina was mysteriously told to "save everybody" and was reactivated, destroying the laboratory and the chamber in which she was sealed. She disappeared after the incident, with her whereabouts unknown to both Donpachi Corps. and Saya, who was still active when she was discovered as one of the few survivors of Element Dolls.

Hina, now going by the name Hibachi, controls an entire weaponry computer system, governing from deep within the technologically advanced City of Ideal, a paradise where humans live in harmony with nature. Believing that the only way to save humankind is to have them adopt a better form, she begins a war to force all humans to become machines. Hastily, the remaining humans of Earth revive the ancient DonPachi Corps to fight Hibachi's army of mechanized people. The new DonPachi's mission is to destroy Hina/Hibachi and her powerful computer system.

If the requirements are met to face Hibachi at the end, she expresses her realization that humans are the ultimate form with her last words.

If Saya is the player's Element Doll, an ending shows Hina damaged and dying in Saya's arms. She tells her she's sorry for everything she has done and thanks her for coming and stopping her before she does something unforgivable. After she dies, Saya cries and after the end credits, Saya is now wearing Hina's ribbons in memory of her and is happy when the pilot comes to her aid.