In the future, young scientist Hiroshi invents an invincible Moldiver super suit, much to the chagrin of evil Professor Machingal - the self-proclaimed best technologist in the world - who is jealous of his pupil's abilities (and whose ultimate evil plan involves collecting rare 20th century technology). In response to an attack on a formula one car restoration exhibit, Hiroshi indulges the power of his suit to save the day against Machingal's forces intent on stealing a rare, fully restored formula one car. Unfortunately Hiroshi's sister, Mirai, discovers Hiroshi's secret identity and changes the Moldiver suit's specifications with a more fashion-conscious lilt. The new suit takes on a girl form, making it impossible for Hiroshi to operate. The fate of the formula one is now in Mirai's hands as Machingal strikes again.

For his studies, Hiroshi journeys to Cape Kennedy, Florida where the space shuttle is about to launch, but the Cape is also playing host to an international pop idol concert. Professor Machingal, who hides under the identity of Mr. Yamagi, Hiroshi's teacher, is there as well, intent on stealing the space shuttle Discovery for his collection and breaking up the pop idol concert at the same time. When Machingal also discovers that the shape of Moldiver corresponds with the body shape of Hiroshi's best friend, Misaki, he erroneously deduces that he must be Moldiver, and includes Misaki's destruction in his increasingly elaborate scheme. And when Mirai learns that Misaki, on whom she has a crush, is also in Florida, she jets from Japan to the orange state, rushing straight into the debacle that's about to unfold.

In television interviews, Yamagi blames Moldiver for the destruction of Tokyo's highways and even rebuts speculation that Machingal (Yamagi's secret identity) shares culpability. He's currently overseeing the reconstruction of the highway system as he conducts clandestine analyses of Moldiver's capabilities and speculates on who its creator might be. Misaki, visiting Tokyo, attempts to deliver an important disk analyzing the Moldiver suit to Hiroshi. Unfortunately the mounting traffic prevents their meeting, so Mirai is called upon for help. She finally catches Misaki before he leaves for space pilot training, but back at home Nozomu - Hiroshi and Mirai's younger brother - discovers the Moldiver technology and begins to work on a Moldiver of his own.

Professor Machingal plans to raise a sunken ship from WWII in order to discover the secret of a dimension barrier to which his grandfather alluded in private memoirs. Nozomu stows away on the salvage ship and discovers intent on helping the professor improve upon what he has learned to be his brother's invention, Moldiver. But no sooner does he offer help than he realizes that Professor Machingal is none other that Professor Amagi, Hiroshi's trusted university advisor. Nozomu then discovers the secret of the dimension barrier and invents something that will make him the "most supreme technologist of all," a title that resonates with evil Machingal's vaulting ambitions. In the interim, Hiroshi analyzes the disk that Misaki gave him, and discovers that Misaki will need a Moldiver in order to survive his next space mission.

With only a ten percent chance of survival, Misaki bravely faces his space mission. Sponsoring the mission Professor Agami, aka Machingal, knows the odds of survival and plans to sabotage his own work in order to save "intellectual" face. Hiroshi desperately works to modify Moldiver for Misaki while Mirai worries about her love. Hiroshi develops a special Moldiver for Misaki just in time for Mirai to deliver it via her Moldiver unit. Machingal's sabotage plans interfere at first, but Mirai finally beats her android attackers. Just as Mirai is set to give Misaki a Moldiver card, a new and improved Moldiver unit shows up intent on destroying all inferior technology.

Mirai fights the new Moldiver and eventually defeats him by infusing their technologies and switching Moldiver cards. She flies into space to save Misaki, but Machingal's last android daughter, Isabelle, tries to exact revenge on Mirai for killing all her sisters. After a bitter battle Mirai defeats Isabelle and saves Misaki.