Juni Cortez, after the events of the second film has retired from the OSS. He now lives a quiet life and works as a private detective, although his salary is very little. One day, he is contacted by President Devlin, former head of OSS, who informs him that his sister, Carmen Cortez, is missing after a mission gone wrong.
Arriving at the technological and computer part of the OSS, Juni is reunited with a now reformed Donnagon and his wife Francesca, who explain that Carmen was captured by the Toymaker, a former OSS informant, the Toymaker was imprisoned in cyberspace by the OSS, but he has since created Game Over, a virtual reality-based video game which he intends on using to escape cyberspace via players that reach Level 5, which is unwinnable. Juni agrees to venture into the game, save Carmen, and shut down the game, given only twelve hours to win. He is also informed that his sister was last seen on Level 4.
In the game, Juni finds the challenges difficult, having only nine lives within the game and already losing one at the start. While roaming a cartoon-like medieval village, he finds three beta-testers, Francis, Arnold, and Rez, who provide him with a passage to the Moon and launch him into space, but mostly to get rid of the competition.
Juni lands on the Moon, losing another life in the process, and receives an opportunity to bring in a fellow ally to assist him. He chooses his grandfather Valentin, who uses a wheelchair and has a personal history with the Toymaker. Valentin receives a power-up which gives him a robotic bodysuit, allowing him to walk and possess superhuman strength and durability. Distracted by a butterfly, he abandons Juni, telling him that they will regroup later. Searching for the entrance to Level 2, Juni ventures into a robot battle arena where he fights a girl named Demetra in order to return to Earth and Level 2. In the fight, he receives a robotic, more powerful suit, and he is placed on a huge mecha to combat Demetra. In the 3-round fight, in which he loses another life, he defeats Demetra and returns to Earth.
He meets the beta-testers again who believe he is a player named "The Guy", who can supposedly beat Level 5. Rez is unconvinced and challenges Juni to a "Mega-race" involving a multitude of different vehicles, which will allow them on Level 3. The only apparent rule of this game is "Win, at all costs". Juni wins the race with help from Valentin, and Demetra joins the group; she and Juni display romantic feelings for each other, with him giving her a med-pack with extra lives and she provides him with an illegal map of the game. Upon entering level 3, Arnold and Juni are forced to battle each other, the loser getting an immediate game over. During the fight, Juni loses almost all of his lives, but Demetra swaps places with Juni and is defeated, seemingly getting a game over, much to Juni's sadness.
