The story opens at Dot's Diner, with Dot running behind schedule, according to her assistant. But, Dot is more upset about Bob and Enzo arriving late for Enzo's "ancient languages" class. Some of the Diner's customers watch as the three argue, with Dot saying how important it is to keep appointments and have everything planned out, while Bob prefers to play it by ear and having fun; Enzo takes Bob's side. The argument escalates until Bob leaves the Diner, vowing never to step into it again, and Dot fumes over Bob's lackadaisical attitude. Enzo is dismayed at their falling out.
The scene changes to Bob's apartment, where Enzo has called Bob on a pop-up window, while Bob is working on his clunker of a car. Enzo asks if Bob is ever going to return to the Diner, but Bob says "no" because he has lots to do. In a series of fast-forwards, we see Bob in various poses of doing nothing, apparently bored, with nobody but "Mike the TV" to keep him company. Mike imitates a dating service commercial, mirroring Bob's obvious loneliness, then impores Bob to "get organized", which causes Bob to throw him out of the building.
Back at the Diner, Dot refuses to call Bob at Enzo's behest, when, suddenly, a tear bursts from one of the Diner's fixtures. Terrified, the customers flee for their lives, but Enzo is thrilled, because it means that Bob will have to come to the rescue. But, Dot insists she can handle it, and, with "Cecil the Server" holding the door, Dot attempts to swat the tear outside, but it explodes on contact, leaving a huge hole in the Diner's entrance, and Enzo, Dot, and Cecil comically charred from the blast.
Enzo and some other Mainframers implore Phong to do something about Bob and Dot. The wise, old Sprite tells them that people are brought together by "tragedy or apology", which gives Enzo an idea.
The scene changes to Bob's apartment, where Enzo suddenly appears in a pop-up window, telling Bob that he has been capture by Megabyte. Unbeknownst to Bob, Enzo has staged the kidnapping with the help of the other Mainframers, with "Megabyte" being just a cardboard cut-out image. Enzo repeats the scam for his sister, Dot, telling her that Megabyte has taken him to "Old Man Pearson's." In a scene reminiscent of old-time movies, the Mainframe stage technicians tie Enzo to a conveyor belt, which leads to a "data eraser", just as Bob and Dot fly in, separately, on their "zip disks". Unaware of the other's presence, they search for Enzo, as a player piano plays old-time suspensful, dramatic, music in the background. As they race to rescue Enzo, they meet, and tell the other that they aren't needed, oblivious to the real danger that Enzo has put himself: total erasure. Enzo's dog, Frisket, saves the day, just as Bob and Dot arrive, still arguing. When Bob insults Dot, she punches him off-camera. Enzo thinks of another scheme to get the two back together.
Back at Bob's apartment, Bob is fuming over the recent event, when his doorbell rings. It is a messenger with a "hologram" card, which shows a tiny, three-dimensional image of Dot apologizing. But, back at the Diner, Dot has received a similar message from Bob.
The scene shifts to "Floating Point", a park, where Dot and Bob sit on a bench, clearly uncomfortable. As they start talking, Enzo and some Mainframers watch from afar. Suddenly, a robotic voice intones, "Warning: incoming game!" Enzo's plan to bring them together seems to have worked, but then Dot and Bob realize they have been tricked.
As the feud seems about to continue, they are enveloped by the game cube, which is a "space-prison escape" adventure, called "Starship Alcatraz." As they argue, one of the prisoners - - the "user" - - steals a key right in front of them. The two reboot into prison guards, just as the prisoner has activated a self-destruct mechanism with 300 seconds on the timer. Realizing the danger, Bob and Dot put aside their feelings, and start the chase. The user turns off the main power, but Dot manages to engage auxiliary power. She then reports that, with the main power off, all the other prisoners are freed, and that the user is heading to the escape pods.
Dot tries to use a logical, ordered plan to defeat the user, when a spider-like escapee suddenly jumps in front of her. Surprised, Dot seems helpless, but Bob shoots the creature with a gun that fires a bubble, encasing the prisoner. Bob tries to tell Dot that there's no time for a plan. Spotting the user, Bob and Dot split-up, each thinking that their way is best. After reaching a higher floor, Dot and Bob are accosted by escapees, one of whom pushes Bob off the ledge. As Dot dispatches of the creatures with her bubble gun, she then shoots at Bob to save him from an imminent demise. Just above her, Dot sees the user, and rapidly fires, just missing him as he runs away. Safely on the ground, Bob uses his wrist device, Glitch, to free himself from Dot's bubble, and then tells Dot that he's on the way to help, but she tells him to stay in the control room to restore the main power. However, Bob can't decipher the control panel, at which point, Dot teases him about his earlier scoffing of Enzo's "ancient languages" She instructs him on what to do, and, together, they restore main power. Using the control panel, Bob directs Dot toward the user, while activating traps to slow down the user: Bob slams a door down on the user, who uses the stolen key to raise the door, but, as he flees up a stairway, Bob triggers it to turn into a ramp, cause the user to slide down.
Meanwhile, Dot cautiously makes her way through the levels, exasperatingly dispatching a group of escapees. The user has reached the escape pod, but, when he opens the door, he finds Dot inside the entryway. She flings him into the pod, and, with the stolen key now in her possession, she casts the pod with the user into space.
Dot tries to figure a plan to get the key to Bob in time to stop the self-destruct, but neither of them knows what to do, when Dot tells Bob that he and Glitch be "ready" for her, as she leaps over the ledge. Not understanding what she meant, Bob looks at the control room monitors, and, to his horror, sees Dot plummeting toward the ground. At a loss as to what to do, Bob exclaims to Glitch, "ANYTHING!", at which point, Glitch detaches from Bob's wrist, and forms a giant spring, cushioning Dot's landing. Dot acrobatically jumps off the Glitch-spring, and inserts the key into the control panel, cancelling the self-destruct with only two seconds remaining. The game disappears. Relieved, Dot and Bob compliment each other over their use of the other's methods to win the game.
The story ends with Enzo, unaware that the two have patched things up, telling the other Mainframers that Dot and Bob will never get back together. But, when he sees them speaking to each other, on friendly terms, his jaw drops, then, referring to the now-chummy pair, utters the word, "Hopeless!"