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.

Mainframe is all but destroyed and Bob realises that their only hope lies in the user.

The battle against Daemon continues, Hexadecimal turns into a sprite, we learn more of the character's pasts, the nulls form an old friend, and Turbo has been infected by Daemon.

The citizens of Mainframe start to battle the supervirus Daemon who has infected 92% of the Net. Bob is horrified to discover that she has infected all the other guardians.

Daemon continues to infect more and more citizens of Mainframe, we discover more about Bob's past and his first coming to Mainframe, Bob's condition worsens, and Daemon learns about love.

Daemon finally infects all of Mainframe except for Little Enzo, Hack, Slash, and Frisket, who were in a game cube. Hexadecimal makes the ultimate sacrifice.

The two bobs try to figure out which is the original and which is the copy. Dot can't decide which one to choose. A game cube drops placing Matrix, Frisket and Normal Bob into a Pokemon style game.

While most of the gang battle Rocky The Rabid Raccoon in a game, Glitch Bob struggles to find a way to separate himself from glitch, and Dot follows her heart.

Dot prepares for her wedding with Normal Bob, Glitch Bob remains comatose in the super computer, and Glitch finally reveals the identity of the real Bob.

Megabyte, now able to shift form, rampages through mainframe, but Bob insists his theories on turning a virus good will work.