Welcome to the city of Mainframe, a computer system inhabited by binomes and sprites who go about their business, trying to keep everything running smoothly. Unfortunately, they live under the constant threat of the user, whose games wreck havoc if left unchecked, and the viruses Hexadecimal and Megabyte, who seek to gain the power of the system's core so they can spread themselves throughout the Net. That's where the Guardian, Bob, comes in. Armed with the versatile key-tool "Glitch" he tries his best to keep citizens safe, upholding his mandate to mend and defend. ReBoot!
Megabyte and Hexadecimal are about to take the core, but Mainframe is saved at the last minute by an incoming game cube. However with Bob gone, Enzo is left having the answer the call of the guardian protocol.
Megabyte is trying to turn Mainfraime against Enzo, blocking him from entering the games and smearing his reputation with propaganda. When the young guardian finally manages to sneak past the blockade, it's more crucial than ever that he wins, this time facing Rocky the Rabid Raccoon...
As Megabyte prepares to launch a another attack using the newly recovered Hexadecimal, Mouse initiates a project to seal Megabyte's domain inside a firewall. Enzo and AndrAIa face the user in a Toy Story-esque racing game.
Enzo and AndrAIa are caught in a tournament style fighting game where they have no control and may not be able to defend against the user.
After getting stuck in a game, Matrix, the hardened and cynical warrior once known as Enzo, and AndrAIa have been wandering the net for a very long time, moving from system to system through the games, searching for a way back to Mainframe. This time they arrive in a barely functioning system, devastated by virals and constant lost games.
Matrix and AndrAIa find themselves on different sides of a conflict between the mysterious Spectrols and a team of super hero sprites.
Matrix is shocked when he finds Mainframe inside a game cube. Dot is there... Phong is there... even Bob! But why did he and AndrAIa reboot as Megabyte and Hexadecimal? And who is Number One?
Having finally found a system with ports to the Net, Matrix is overjoyed. But it doesn't last long, when access is blocked as the city comes under siege by a team of... guardians?
Matrix and Andraia meet up with Captain Capacitor who promises to help them find Bob as long as they release his crew from the prison in which the guardians have placed them.
The crew of the Saucy Mare enter the web looking for Bob but when a web creature sucks away half of AndrAIa's energy, leaving her in a dying state, Matrix must find the creature so he can save her life.
The Saucy Mare is attacked by a group of degraded sprites riding web creatures, and AndrAia is saved by an old friend.
The traps Mouse once placed to stop the web creatures from accessing Mainframe are now making it difficult for the sprites to return home.
Matrix and the gang finally return to Mainframe only to discover it has been almost destroyed by Megabyte. We learn what the resistance has been doing all this time and the plan to finally save their home.
The battle for Mainframe begins and Matrix has a final confrontation with Megabyte. Meanwhile, Hexadecimal seems to have gone even more insane but Bob thinks he might be able to help her.
Mainframe begins to crash around them and users from games played break out into mainframe. Matrix meets up with an enemy from his past.