Megabyte tries to blackmail Bob into stabilizing a tear into a portal to the super computer. As Bob makes an escape with the help from Dot the user inserts a game which stabilizes the tear. Bob and the rest of the sprites must race Megabyte, who has infected the user, to the portal to win the game and keep him from gaining access to the super computer.

An accident causes a magnet to drain Dot of energy and, according to Phong, the only way to save her is to feed her slow food from Al's on level 31. While in Al's, the sprites are caught in a medival fantasy game where Bob and the user are attempting to reach Dot, the damsel in distress. Or are they?

After Bob makes Dot late for an appointment, she and Bob get into a big argument. Seems Dot suddenly thinks Bob is too "random", and Bob thinks Dot is too straight-laced. Enzo and the other citizens of Mainframe try to trick the two into making up, but nothing seems to work. When Bob and Dot get trapped in a game cube, will that be enough of a crisis to get them to stop squabbling?

Megabyte takes advantage of Enzo's new delivery service to try to deliver a delete command to Hexadecimal. Bob unknowingly attempts to deliver the package, only to be trapped in a racing game where the user's vehicle becomes a ticking time-bomb.

Megabyte steals Hexadecimal's precious Medusa Bug but finds it to be a trap which turns everything in Mainframe to stone.

Mike the TV is driving everybody insane, but when a game cube drops and Mike reboots into a warrior they're going to need him to help stop the user.

Dot is arranging a celebration for Enzo's first birthday, and Bob has to keep the young sprite occupied until everything is ready.

Mainframe is thrown into utter chaos when Hexadecimal manages to tap into the system's paint function.

Two special agents from the CGI are investigating disappearances in level 31. Their prime suspect is Mouse but the real abductor ends up being something far more dangerous: a web creature. The Guardians would destroy all of Mainframe to kill the web creature, but Bob has other ideas.

Frisket swallows an unformat command Megabyte had just uncovered. Wanting to get it back, the virus has Enzo kidnapped, using him as bait to lure the dog into Silicon Tor.

After Bob upstages him during a game, Enzo decides to get smarter in a hurry. The Read-Only Room at the Principle Office is too much like work for the young sprite, so he's tempted into tinkering with the system clock. Only instead of making himself twice as smart as everyone else in Mainframe, he accidentally makes everyone else half as smart! What's worse, he ends up trapped in a game cube with a bunch of his dumbed-down friends. Can Enzo best the user by himself and fix this mess?

Mainframe is attacked by dastardly software pirates, who quickly scavenge the city, taking everything of worth - including Bob!

A being of incredible power, known as a codemaster, arrives in Mainframe, demanding they bring out another codemaster who he believes is hiding there.

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 Pokémon style game.

With the help of Mouse, a hired mercenary, Megabyte intends to send a heavily compressed ship into Bob's head to take control of his brain. However, things don't go exactly as planned.

Dot manages to convince the binomes of one of Megabyte's sectors to entrust her with their PIDs, so she can register them with the Principal Office. But first she has to get them safely back to Mainframe, which proves harder than anticipated when the virals attack the meeting place. And if that wasn't enough, she keeps getting mysterious flashes of a reality where Megabyte has taken control of the system.

Megabyte is draining energy from the games to fuel his attempt to breach the Mainframe archive's protective barrier. But when he takes too much, the game crashes and merges with a new one, trapping him and Bob inside the chaos.

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...

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.

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.

With Dot stuck in a game, heavily depressed and about to give up, Phong decides to take drastic action, sending her into a possible future where she lost the game and got herself and Bob nullified.

The joy of receiving a new upgrade is cut short when it turns out to contain Megabyte himself, who's decided to take a more direct approach to infecting the core.

Megabyte makes a grab for the core energy, but ends up getting trapped with it inside a corrupt game. Now Bob must keep the game going until he can get the energy back to the Principal Office or Mainframe will shut down when game ends.

Enzo is feeling along since there are no sprites his age in Mainframe. Dot won't let him enter games with Bob and Frisket comes and goes has he pleases. So when a game cube drops on the Diner and he runs to a young female sprite named AndrAIa, he's all too quick to make friends with her. But there's something Enzo doesn't seem to realise about AndrAIa...

Mike accidently shatters Hexadecimal's looking glass, unleashing a horrible black parasite that infects the virus. Suddenly, all the nulls react, flocking to Lost Angles, covering the altered Hexadecimal until she's became a gigantic mass of nulls, walking around and flattening random buildings.