The story jumps forward to the next day, when the alarm clock goes off, throwing Bob into the shower and hair styler (where he emerges with gold plated hair). A panic call comes in from Enzo, who informs Bob that Dot's Diner has been trashed. (Signs down, windows broken, tables overturned.) While the group is overlooking the damage, Megabyte shows up in a Double Sided Vid Window. As long as Bob does one little favor, MB will try to make sure that this sort of thing won't happen again.
The standoff is interrupted by an incoming game. Megabyte orders his legions to make sure that Bob does not play a game until the favor is done. They are successful at keeping Bob out, and this time, the User wins. The entire sector is off-line and nullified. (There is a big dark hole where the Game cube had been, and the sprites that had been in the game are no where to be seen.
Bob goes to see Phong at Dot's request. After defeating Phong at a game of Pong, Phong explains that COMMAND.COM has tried to eliminate Megabyte at every upgrade, but the virus is very clever and has bad file servers in every sector.
Bob shows up at Megabyte's Tor and is very convincing at being impressed with MB's power. Down in the lower levels, Megabyte has massed an army, hundreds of tanks and thousands of viral binomes, waiting for a door and a bridge to be opened. MB has partially controlled a Class 12 tear leading to the Super Computer. (The tear is a large, nebulous ball of flashing blue and white light.) The favor is for Bob to stabilize the tear into a portal. (Only games dropped by the User and Guardians are able to stabilize a tear.) Bob proves that he can use Glitch to create a portal, but is yanked back by the leash that Megabyte has put on him. Hack and Slash show up carrying Dot, and during the distraction Bob knocks over the control console, allowing the tear to break free.
Just then another Game cube descends, to Megabyte's delight. The Game takes place on an aircraft carrier, and Megabyte infects the User's fighter craft. "Alpha wing clear of deck; proceed heading 1138, stay frosty." The tear has been stabilized into a portal at the end of the third level.
The battle goes through an asteroid field, much like the one in Star Wars, and Dot fires the shot which destroys the battle cruiser at the second level. The third level is an ice tunnel, which takes out all but three ships; Bob, Dot, and Megabyte. During the battle, MB's ship is shot down, he slices the wing off of Bob's ship, which takes out Dot's ship. Bob ends up hanging from a stalactite, then uses Glitch as a rope to get over the portal and drop in. This ends the game and destabilizes the tear. MB threatens Dot with some really nasty fingernails, but Bob comes back, and the tear/portal disappears completely. Bob boasts that this was a result of a command that he picked up at the Super Computer's armory, and sets off another two commands to make him and Dot disappear. Megabyte assumes it was a RETURN command and orders everyone back to the Diner. When he leaves, an invisible Bob says "hidden file commands, ya gotta love 'em."
Later, at the Diner, Bob says that Supercomputer was a nice place to visit, but he'd rather stay in Mainframe. Cecil complains that it is not his function to clean up, as more pieces of the Diner fall down.