Fry is preparing for a mission, only to learn that Bender and Leela had just returned. Not only finishing the mission but doing it even better than usual since they earned medals for the mission while he was looking up curse words in the dictionary. While the latter clean themselves up, Fry states that they could've needed him but Bender denies it. Fry has the last laugh after tricking Bender into denying that he is great.
While Leela is on her date with Chaz, the mayor's aide, Fry walks Nibbler for her. Fry feels that he is useless, only to have Nibbler tell him otherwise. Nibbler knocks Fry out, drags him to his small spaceship, and takes him to planetEternium. After being introduced to the Nibblonians, Fry's learns his importance; he has a unique genetic disorder which resulted in him lacking the delta brainwave due to him becoming his own grandfather. This rendered him immune to the attack of the Brainspawn a few months ago, an attack which no-one else on Earth remembers.
The Nibblonians reveal the Brainspawn's plan: to collect all knowledge in the universe and destroy it so no new information pops up. Fry, because of his immunity, is the only person who can stop them. In other words, Fry is the most important being in the universe. The Nibblonians have made a quantum interface bomb which will send the Infosphere into an alternate dimension forever. Fry's mission is to implant it inside the Infosphere. The Nibblonians bring Fry to the Infosphere just as it collects the last of all the data in the universe. It opens to scan itself, the final piece of information. This is the only chance to get in, so the Nibblonians send Fry in on the Scooty Puff, Jr.
Fry arrives at the center of the sphere, rendered invisible by his genetic abnormality as long as he avoids intense thinking. He is about to activate the bomb, but realizes that while he is there, he can find the answers to any question in the universe. He asks questions: "What's stamp glue made of?" and "What killed the dinosaurs?", which answers toad mucus and that the Infosphere himself killed the dinosaurs respectively. Fry is discovered and the Brainspawn try to stop him, but his immunity protects him. He tries to escape, but the Scooty Puff Jr. falls apart, trapping him. The Brainspawn identifies Fry as "The Fable One" and gloat that he cannot escape. Their laughing ceases when Fry holds up the bomb and activates it. The Brainspawn remind that him that he is doomed to enter the alternate universe with them. One brain adds that they'll also form a clique that Fry won't be part of. But Fry boasts that he is glad that his life had a purpose: "Leading good to victory over evil".
The Brainspawn question his motivations, suggesting that the Nibblonians are not as good as they appear. They suggest that Fry inquire about the night of December 31st, 1999, the date Fry got frozen. Nibbler nervously tells Fry not to ask, saying that it would be boring, so he concedes, only to be urged by the Big Brain. It is revealed that Nibbler unbalanced the chair that Fry was sitting on that night, tipping him into the cryogenic tube and bringing him to the future. Nibbler explains that Fry was the only person who could carry out the mission against the Brainspawn's Infosphere. As Fry grapples with the shock that the Nibblonians ruined his life, he and the Infosphere are sent to the alternate universe.
Meanwhile, Leela is on a date with Chaz, having a luxurious dinner at Elzar's Fine Cuisine. Chaz reserves the rocket ice rink specially for Leela, denying its use to the orphans who were supposed to visit the rink. Leela, having grown up as an orphan herself, tries to persuade Chaz to allow the orphans to use the ice rink, but he refuses. Leela realizes that Chaz abuses his position and completely ignores the needy. She shoves his badge in his mouth and leaves.
In the other dimension, the Brainspawn decide to spend their eternity singing American Pie. Fry, on the other hand, wishes that the Nibblonians hadn't froze him. The Infosphere informs him that it is possible for him go back in time to stop Nibbler from freezing him. The Infosphere explains that there is a nexus point between dimensions at the space-time that he entered the cryogenic tube and only Fry can return there. The Big Brain endorses this, as it would be a win-win situation - Fry can have his old life back and the Brainspawn can understand and destroy the universe a millennia later. Fry accepts their offer. The Brainspawn then begin calculating to send Fry back. Fry asks the Brainspawn if they check their calculations. The Big Brain says "Our calculations are always correct, for we are gigantic brains." and Fry is transported to the cryogenics lab.
On December 31st, 1999, Nibbler places a prank order for I.C. Weiner. But future Fry appears behind Nibbler under the desk, just before his past self is frozen. He restrains Nibbler, who is confused at this paradox. Fry assumes that Nibbler has traveled through time as well, but Nibbler explains that his people lack that ability, but possess longevity, and Fry first met Nibbler when he was a thousand years older. However, Fry refuses to let himself be frozen. Nibbler pleads that the Nibblonian sages have foreseen that in a thousand years, the universe will depend on Fry. Because he would have died of old age almost a thousand years before the mission was to take place, they had to freeze him in 1999. Fry points out that they could've asked him; Nibbler says that they were afraid that he would refuse. Fry denies it, saying he loves the future; the Nibblonian then asks why Fry is choking him right now; Fry asserts that he doesn't "like being used" and puts Nibbler down. Leaving the choice to Fry, Nibbler asks if there is anything he wants to save in the future and Fry realizes the only thing worth saving is Leela. Fry mentions this to Nibbler, who mysteriously notes that Leela may be the "Other", and advises Fry not to give up on her. He promises if Fry makes the right choice, back in the 31st century Nibbler will help Fry win Leela's heart. As New York counts down to New Year's, Fry gives in and unbalances the chair himself, freezing his past self. Before he fades away, he yells "Just remember that Scooty Puff Jr. sucks!" Nibbler vows that "in a thousand years, I'll get right on it".
Back in the 31st century, Fry escapes the InfoSphere on a Scooty Puff Sr. and Nibbler returns Fry to Earth, blanking Fry's mind of what happened to remain undercover, but not before handing Fry a flower. At Planet Express, Fry gives Leela the flower. Leela, touched, gives Fry a kiss.