The story opens with a game cube already having landed in the city of Mainframe.
The scene shifts to Megabyte's lair, where the villainous Megabyte impatiently awaits the arrival of a female sprite named 'Mouse'. She appears, seemingly from nowhere. As she climbs aboard a tank-like vehicle, Megabyte tells henchmen Hack and Slash that she is in charge of the unrevealed "mission". When the two enter the vehicle, Megabyte activates a "compression field", which shrinks the ship and its occupants to near microscopic size. MB puts the now tiny ship inside an eye dropper, and transfers it via a pop-up "vid window" to one of his operatives, who is at an undisclosed location.
Back at the cube, an off-screen voice announces "Game over", and the cube rockets skyward, leaving a few sprites cheering Guardian Bob. Bob, with friends Dot, Enzo, and Frisket, head to "Level 31", to relax at Al's Diner, unaware that they are being watched by Megabyte's operatives. At the diner, Bob orders a "quantum shake". Unbeknownst to anyone, Megabyte's henchmen have tied-up the diner's chef, Al, and one of them puts the shrunken ship into Bob's drink, then transfers the drink to the waiter, who hands it to Bob, only to be blocked by Enzo, who asks Bob if he can have a sip. Bob allows him to do so, and, as Enzo sips the drink, we see the ship being swallowed into him.
Mouse reports to Megabyte that all is going to schedule. Megabyte gloats at a video screen displaying an image of Bob with peculiar lines running through it, saying that he'll finally have access to Bob and the Supercomputer. When the ship lands, somewhere inside Enzo, Hack and Slash exit, and accidentally fall down a hole. As they struggle to get out, their actions accidentally affect Enzo by making him move about in a random, uncontrollable, and comical fashion. Worried, Bob and Dot take him to Phong for an examination. When Phong inserts a viewscope into Enzo's ear, he is astonished to see Hack and Slash. Bob volunteers to shrink down and battle them.
Meanwhile, Mouse deploys a control device, and Megabyte switches it on, remotely, gloating about his impending victory. But, when he hears a child's voice speaking about club passwords, no girls being allowed, and a lame excuse to a teacher about the dog eating homework, Megabyte realizes something is wrong.
Bob, astride a hovercycle, is shrunk by Phong, who puts him in Enzo's ear.
Megabyte, confused by the turn of events, orders Mouse to move the unseen host to a reflective surface, where he sees that it is Enzo who had swallowed the ship. At first, Megabyte is upset that his plans to take over Bob's body are ruined, but then he realizes that Enzo is inside the "Principal Office" and the "core". Megabyte takes over Enzo's body, and steers him to the core. Mouse becomes suspicious by Megabyte's actions, but she is interrupted by Bob, attacking the ship from his hovercycle. Hack and Slash use their jet packs and missiles to attack Bob, but they are no match for him, and they end up smashed to pieces inside the ship. Bob lands and enters the ship, where Mouse surrounds him in a stasis field.
Meanwhile, Enzo has reached the entrance to the core, where a voice warns not to enter. He struggles to stop, but Megabyte's control overwhelms him, so he has no choice but to enter the vault-like room. As the huge door closes behind him, Dot and Phong just miss him, and Phong laments that the Mainframe is doomed.
As Megabyte tends to something off-camera, Mouse removes part of the stasis field to see the face of whom she has captured, and is surprised to recognize Bob, who is equally surprised to see her. He chastises her for her actions, which will lead to their destruction. She believes and releases him, then contacts Megabyte for verification. Megabyte assures her that everything is fine, but she realizes he is lying, so she disconnects the control unit, freeing Enzo, who runs away from and out of the core.
After Mouse and Megabyte exchange heated words about her treacherous actions, Megabyte turns off the communicator, just as an off-camera voice warns that the ship's compression field is destabilizing. With Bob at the ship's navigational controls, he and Mouse use the ship to pick-up the control unit, disintegrate Bob's hovercycle, then speed off to leave Enzo's body before they regain their normal size.
As they race through Enzo's insides, Mouse flirts with Bob, much to his embarrassment. A few moments later, Mouse says that they are almost "there", just as Enzo is seen about to sneeze. As the ship starts to enlarge, its occupants start to scream in dismay, but when Enzo sneezes, the ship appears in its full size, expelled from Enzo's nose, and everyone is safe.
When the ship's door opens, Phong, Dot, and Enzo are relieved to see Bob, but a jealous Dot demands to know about the girl beside him. As Bob introduces them, Mouse has vanished, apparently escaping the Principal Office, leaving Bob at a loss for words. Still in pieces, Hack and Slash apologize for their behavior, while Bob and Phong smile with a tacitly agreed on plan for the two henchmen.
The story ends at Megabyte's lair, with Megabyte wondering where his two henchmen are. As he looks around, Hack and Slash are seen by his feet, fully repaired from their battle with Bob, but have been shrunk to comic effect.