Bob and Dot fight to keep Megabyte from harnessing the power of a recently discovered, unusually large, "Tear". They nearly succeed, but a game unexpectedly drops down, enveloping them along with the tear, which has become a portal to the Supercomputer. Dot and Bob must defeat Megabyte inside the game, or he will escape through the stablized tear, infecting other systems and becoming more powerful.
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 a 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.