Glitch Bob, Matrix, AndrAIa and the Software Pirates return from the Web to find Mainframe devastated by a war between Megabyte, Hexadecimal and the Mainframe resistance.
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.
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.
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.