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.

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.

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.

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.

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.

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.

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?

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

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?

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.

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

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?

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.

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

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.

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.

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

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.