The remaining inhabitants of Mainframe have survived Megabyte's bane, but the system is destroyed and dying. As their final hope they must cause a full system crash to spur the User to perform a restart.
The Mainframe resistance devises a plan to take back the Principal Office. Matrix alone faces Megabyte, who is trying to access the Web. Meanwhile, Glitch Bob gets tied up with Hexadecimal.
A portal to the Web hovers over Mainframe, and its citizens must prepare for war. Due to the situation Bob gives Enzo a commission as a cadet guardian. Megabyte and Hexadecimal join the battle, but they have a secret ulterior motive.
The entity that came through the looking glass attacks and corrupts Megabyte, who then merges with Hexadecimal, transforming the two of them into Gigabyte, the next generation of virus.
In his quest for dominance, Megabyte continues his propaganda campaign against Enzo and those that remain in the Principal Office while the rest of Megaframe is defenseless against the destruction.
Matrix and AndrAla finally land in a system that has ports to the Net, Matrix meets Guardian Turbo, who explains that a dangerous virus named Daemon has infected all Guardians save for Bob and Matrix.
The group take refuge in the Principal Office, fending off Megabyte and Hexadecimal's onslaught on the city. A game cube inadvertently interrupts the attack. Enzo, unable to resist his Guardian protocol, enters the Evil Dead inspired game.
Matrix is ready to give up his search for Mainframe when it seems he's found it in the form of a game. When AndrAla and Matrix reboot, they take the form of Megabyte and Hexadecimal. The goal of the game: find number one.
In an attempt to save Mainframe from complete system shutdown, the sectors must be powered down. Glitch Bob enters the core to keep the Principal Office online. Tears begin opening all over the city, releasing saved Users from past games.
While hunting for the Web creature that bit AndrAla, The Saucy Mare engages in a full-blown battle with a swarm of the monsters. Just when it looks as though all hope is lost for the crew, a new protector arrives.