Above Mainframe hangs the web creature's parting gift: A gigantic portal to the Web - a chaotic abyss filled with unspeakable horrors. It will take the combined might of all inhabitants of the system to close it, including the viruses, but can they be trusted?

The infected Megabyte merges with Hexadecimal, turning into the energy devouring super-virus Gigabyte. It must be stopped before it gathers enough power to create a portal to the Net.

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.

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

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 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 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...

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.

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.

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.

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.

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

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.

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.

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.

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.

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?

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.

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.

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.