After being punished with no more television, Timmy wishes himself into the world of television to escape the harsh reality of his life and his parents. Unfortunately for him, his carelessness with magic leads to Vicky taking over the world in the future, and now Timmy must stop her to prevent the destruction of Dimmsdale, while escaping a mysterious masked man that is trying to track him down.
20 years in the future, A.J. prepares a time belt to use. Chester and A.J., who have grown into buff muscular rebels, are racing through the ruins of Dimmsdale on a hover board (the cityspace has become a parody of "The Terminator" and other dystopian futures such as the Dragon Ball Z (Kai) TV special, The History of Trunks), while a mysterious masked man chases them. They fire lasers from devices strapped to their hands at each other, destroying much of the damaged city as they do this, including Timmy's old house, the head of a statue of Chompy the Goat, Dimmsdale Elementary School (Chester and A.J. destroyed it intentionally), and Chester's trailer while Bucky is still inside and sitting on the toilet. The masked man pleads to Chester and A.J. to give up, but they believe it is a trap. Chester stays behind and tries to stall the masked man, holding his father's prized bat, but the masked man easily dispatches him and zaps him with a laser, freezing Chester in stasis. A.J. has gotten ahead, and managed to make it to his old house where he completes a time belt so that he can go into the past and prevent the bad future from ever happening. But before he can get underway however, the masked man freezes A.J. and takes the belt from him. A robed figure appears behind him, who gloats about having the time belt to use for her own power. The robed woman pulls her hood back to reveal it is Vicky, now the Supreme Ruler of the World (she is later seen in attire similar to dictators like Adolf Hitler, Fidel Castro, and Joseph Stalin). She sends the masked man back in time to prevent Timmy from stoppingher.
Back in the past, sixteen year old Vicky is preparing a backpack full of torture items for when she babysits Timmy. She laughs about being the Supreme Ruler of Hating Timmy, and leaves to go babysit him, while a news editorial by Chet Ubetcha begins airing on the TV. He is warning adults about violent TV and how it is affecting kids. Chet particularly blames a program called "Maho Mushi", a Japanese anime-type fighting show resembling Dragon Ball Z Kai . Timmy had an idea to help this conception when he wishes for a spaceship known as the Kid Crusher (a parody of The Star Destroyer from the Star Wars films), from the program into his world and flies it around Dimmsdale, raining destruction and causing widespread panic on the streets below. When he starts to crash, he wishes himself into a "Banzai Bubble" from his Maho Mushi cards and then starts plummeting toward his Dad's office. Inside, Mr. Turner was on hard work cleaning his office, and is about to win the cleanest office award when Timmy comes crashing in, bounces around the office, completely trashing the place before bouncing back out, leaving a shocked Mr. Turner behind, who is even more horrified when the boss comes in, sees the office trashed, and immediately gives the award to his arch-rival and next door neighbor, Sheldon Dinkleberg. Elsewhere, Mrs. Turner is about to sell Billy Joel a glass house (a reference to his album Glass houses), when Timmy collides into it causing it to shatter, just moments before the transaction was to be completed. All that remains now is a pile of broken glass. Mrs. Turner hangs her head in disappointment, and says "I'll get a broom".
Running through the streets, Mr. and Mrs. Turner bump into each other while looking for Timmy, the cause of their problems. It doesn't take long before he comes to them, landing on top of both of them before his Banzai Bubble pops. Mr. and Mrs. Turner stare at Timmy angrily after Timmy falls to the ground and is about to be punished, while something happens in a nearby alleyway. A green light and electrical sparks fill the alley, and the masked man from the future appears. He spies on Timmy, who is being dragged away by his enraged parents. Before he can get out of the alley though, two police officers pull into the alley. The masked man jumps into a nearby dumpster and hides, but the cops come by and sit on the dumpster so they can talk and enjoy donuts for "hours and hours on end". Meanwhile at Timmy's house, Mr. and Mrs. Turner scold Timmy for mimicking a violent television program. Mr. and Mrs. Turner told Timmy to not watch Maho Mushi anymore and watch an educational program, like "Dictator Week" (a parody of World War II history) on the Biographical Channel, (a parody of the History Channel), but Timmy refuses. This makes Mr. and Mrs. Turner angry when they realize that they cannot trust Timmy to not mimic television, and therefore they cannot trust Timmy with television at all and so, they ground Timmy with no more television, and leave him with Vicky (as usual) to watch him and make sure he is forbidden to watch television.
Before Mr. and Mrs. Turner can leave Timmy with Vicky in their usual time, this time, Timmy begs his parents not to leave him with Vicky, and that she is evil. Mr. and Mrs. Turner briefly suspect something about Vicky, but they shrug it off after Vicky showers them with cheap gifts she got. Mr. and Mrs. Turner run off to gloat about their gifts to Dinkleberg. After Mr. and Mrs. Turner left the house, Vicky begins to chase Timmy into his room with a flame thrower, while doing that. Timmy barricades his door behind him, and then sarcastically asks his fairy godparents what he should do now that his parents punished him with no more television. They take the hint, and poof up Timmy a television. However, Wanda still scolds Timmy about disobeying his parents, so Timmy decides that he isn't watching TV if he is in the TV, he wishes for a remote that allows him to go inside TV. Timmy explores a few channels, first a cartoon about the future called the "The Futurellis", (a parody of The Jetsons), then a cartoon called "Carpet Critters", (a parody of fellow Nicktoon program The Rugrats), and then a cartoon called "Heavy Hal", (a parody of Fat Albert). Even going so far as using a parody of the pooperscooper. Cosmo and Wanda watch Timmy as he interacts with the TV programs he explores, when Vicky comes and tries to bust down Timmy's door. Cosmo disguises himself as Timmy and does a bad job at hiding the fact that Timmy is trying to sneak in and watch television again in his room. Vicky takes a photograph of "Timmy" next to the TV and decides to tell on Timmy.
Outside of Timmy's house, the masked man is stalking Timmy. He mistakes Cosmo for Timmy at first, and is then blinded by the reflection of light from a plaque that Vicky gave Mr. Turner, who was showing it off to Dinkleberg. Sheldon pulls out an even brighter plague that nearly blinds Mr. Turner and melts part of his clothes. Mrs. Turner gets a call from Vicky, who says that Timmy not only immediately turned on the television after they left, but also caused a variety of other destructive events such as breaking the vase, shredding the family pictures, burning the piano, and writing "My Parents Stink" and "Dinkleberg Rulz" on the living room walls that were really caused by Vicky herself. Mr. and Mrs. Turner became so angry they erupt in a nuclear explosion, blowing the top off Dinkleberg's house off as they shouted Timmy's name. Vicky is satisfied with her dirty work, and runs off to get her camera so she can record Mr. and Mrs. Turner. Back inside TV, Timmy is in another cartoon called "Jonny Hunt", (a parody of Johnny Quest). Timmy is happy that the adults in that program will allow a 10 year old boy like him to go on dangerous missions, but not without giving him a dangerous weapon first. Timmy takes the rocket launcher they gave him back with him to the real world so that he could show Cosmo and Wanda. Timmy returns to the real world and shows Cosmo and Wanda the rocket launcher he got from television. When Wanda sees that Timmy brought a dangerous weapon back to the real world, she reminds him he could get hurt, but Timmy doesn't think so and says, "Not as long as you guys are around." But Cosmo remarks that they won't always be around and Wanda shushes him while Cosmo is in the shower and Wanda flushes the toilet to get Cosmo out of the shower and he lands in the toilet. Timmy is curious to what Cosmo meant though, so Cosmo tells Timmy about a story called "The Wands and the Wings" where he holds up a green sock puppet and a pink sock puppet, but Wanda tells Cosmo it's the wrong kind of speech and explains about what happens when god kids grow up.
Wanda poofs up a movie screen and it shows a little blond girl receive fairies, disguised as two pet hamsters. However, when the girl grows up, she no longer believes in magic and no longer needs fairies, the fairies are called back to Fairy World and the hamsters are replaced with normal ones. Wanda explains that the length godparents spend with their godchildren depends on how much their godchild believes in them, but they'll eventually have to leave when Timmy becomes an adult. This upsets Timmy when he realizes that he will one day forget all the adventures he had with Cosmo and Wanda. To make matters worse, Vicky burns down Timmy's barricaded door with a flame thrower with his angry parents in tow about to punish their son. Timmy accidentally fires the rocket launcher he brought back from television, blowing the roof off and destroying and the upper floor of his house. Mr. Turner's boss comes by with a "Cleanest House" award (The same moment where his boss was about to give Mr. Turner the cleanest office award before he gave it to Dinkleberg due to his office being trashed by Timmy earlier) and sees the place even more trashed, so he tosses the award to Dinkleberg instead and leaves. This infuriates Mr. Turner to its peak (He becomes even more angrier that he pulls his hair out very hard and his head is bald when he realizes the rocket launcher is out of ammo and he cannot fire it at Dinkleberg's house). Vicky runs off with Timmy's magical television controller (Mr. and Mrs. Turner gave it to Vicky because Timmy tried to watch television again even though he was grounded from it), and Timmy is grounded again by his angry parents. Mr. and Mrs. Turner then angrily leave to go get ammo for the rocket launcher in order to fire at Dinkleberg's house. Vicky takes her chance to take a picture of Timmy being miserable after his angry parents yelled at him for trashing the Turner household while they were away which she lets Timmy keep because it's for him. She then takes a picture of Timmy in a Bo Peep costume for the internet, and then Vicky removes the Bo Peep costume on Timmy and she quickly leaves the trashed Turner house with Timmy's magic remote she has in her hand.
Timmy is now angry about his parents not believing anything he says about Vicky and punishing him for all the things that he did not do. Wanda tells him that they're just trying to raise him to be a responsible adult as everyone has to grow up. However, Timmy contradicts her visually by the characters he watches on TV as they've stayed the same age even after a couple of years. Timmy then realizes if he is in television and stays as a kid forever then he won't have to lose his godparents for a couple of years. He decides to run away from home and he is going to do so through television. He wishes for another magic remote to replace the one that was taken away by Vicky and decides to live in television. He writes his parents a "Goodbye Foreveur" (Ever is misspelled by evur by Cosmo because he claims it adds effect) note and then zaps himself into the TV along with Cosmo and Wanda who accompany him while he stays in television forever. However, the masked man was watching the whole thing, and he follows Timmy, Cosmo and Wanda into the world of TV. Mr. and Mrs. Turner came back to the room with ammo and begin to take Timmy's TV out of his room and use the rocket launcher with ammo to fire at Dinkleberg's house, but instead they find the note and realize their son has ran away, but Mr. Turner also realizes that his son would spell Dinkleberg after misspelling Forever in the "Goodbye Foreveur" note. The masked man is chasing Timmy through the TV channels, when he crashes into the wrong channel cube and ends up in a children's cartoon called "Paula Poundcake", (a parody of Strawberry Shortcake). He grabs a candy cane from the environment and attempts to use it to fend off the "little frosted freaks". Meanwhile, Timmy and his fairies have arrived in "Walnuts", (a parody of Peanuts). They landed right in the middle of a Hanukkah Special. Another kid near Timmy faints when the adults come, and they blame Timmy (speaking in unintelligible dialect like the adults in Peanuts) who pleads he is not responsible for the kid lying on the ground, but they decide to get the police involved and the room is suddenly flooded with tear gas. Timmy remarks that the adults ruined this place too, so he decides to find another channel. He decides to go into "Space Spectre", (a parody of Space Ghost).
Back in the real world, Vicky is watching Timmy, Cosmo, and Wanda fool around in the TV (she doesn't know it's them yet) and considers the programming to be boring. She fools with the remote she took from Timmy, it's magical properties cause it to merge a political debate show (a parody of Politically Incorrect) with a wrestling theme (a parody of WWE), much to Vicky's entertainment. She realizes that the remote can do magical things, and changes the channel to a contest show (a parody of Wheel of Fortune). A man is about to win 1,000,000 and he says he'll give it all to charity, Vicky is disgusted by this and screams "Why can't that be ME!?" and pounds on the remote in frustration. The remote zaps her into the TV contest and she is handed a bag of money, but the host takes it back when its pointed out that Vicky is 16, not 18 because she is too young to participate in the TV contest. Frustrated, Vicky smacks the remote again, pressing the fast forward button and aging her to 18. Vicky is now able to take the contest money, and she also begins to realize the power of the remote. She wants to go to the Dictator Week program on TV so that she can take over the world, which makes the host think she's really happy and on fire.
Still inside the Space Spectre cartoon, Timmy and his fairies are about to be captured by the masked man, who has tracked them down. The masked man demands the remote, promising that he will send Timmy back home unharmed, but Timmy refuses and manages to use his remote to escape the channel. His next destination is "The Meatflints", (a parody of The Flintstones). The masked man continues to chase Timmy through other programs including "Go Go Racer" (a parody of Speed Racer), "Snooper Dog and the Clue Crew" (a parody of Scooby Doo) and "Blackbird and Sparrow" (a parody of Batman and Robin). Back in Dimmsdale, Mr. and Mrs. Turner are questioning Chester and A.J. about Vicky, and whether she is really evil. however, a Few Hidden Cameras secretly appear on both A.J. and Chester. A.J. hesitates, but Chester is about to spill everything to Mr. and Mrs. Turner. (even Smashing one of the Hidden Cameras.) Before he can though, a bracelet around his ankle shocks him and dispenses a slice of cheese to distract Chester. Mr. and Mrs. Turner continue to find more answers about Vicky's evil nature but Mr. Turner snatches the cheese from Chester before he continues to be zapped. Meanwhile in the Blackbird cartoon, Timmy is living the life inside Blackbird's mansion (a parody of Wayne Manor), when the masked man attacks him again. This time, Timmy manages to corner the masked man in the Birdcage (a parody of The Batcave). The masked man takes off the mask, and the man is revealed to be Timmy himself, from the future.
Future Timmy reveals that Vicky used the remote to get to dictator week, take over the world, and turned Dimmsdale into a desolate wasteland. Sneaking into the ranks of Vicky's troops, Adult Timmy managed to become Vicky's most trusted soldier. He was sent after Adult Chester and A.J. who were inventing a device to go back in time and stop Vicky. Once A.J. completed the device, Timmy took it so that Vicky would send him back in time with it and not suspect anything. The future Timmy needs to stop Vicky and destroy the remotes so that the future will change. Present Timmy is unconcerned with this at first, he doesn't care about home and Dimmsdale anymore, as long as he is safe inside television. However, Vicky has tracked them down inside television, and begins to attack them. They manage to escape Vicky, and Timmy shakes hands with his future self, agreeing to put a stop to Vicky and prevent her from destroying the future.
Mr. and Mrs. Turner continue to look for answers. They go to Vicky's House and decide to talk to Vicky's dad and mom directly, but they are no help, when arrays of Lasers are on them. They are completely terrified of their daughter, and push Mr. and Mrs. Turner out the house the moment they realize they might suspect something of her. Tootie is watching from her room above and overhears that Timmy is missing because of Vicky, she decides to take matters into her own hands. She throws a cryptic message attached to a Timmy doll through the window of the Turners' car, asking them to meet her at the Dimmadelphia Cable building, disguising her name as "Deep Toot", a reference to the Watergate scandal whistle blower Deep Throat. Mr. Turner cracks up at the sound of her funny pseudonym and Mrs. Turner doesn't get it. In the TV universe, Timmy, Cosmo, Wanda , and future Timmy chase Vicky through some more programs, including "Clint's Hints" (a parody of Blue's Clues), "Ted and Jimmy" (a parody of Tom and Jerry), "Rabid Rabbit" (a parody of Looney Tunes), and an unnamed Christmas special, (possibly parodies of Rudolph, and Frosty The Snowman). "The Feldmans" (a parody of The SimpsonsButch Hartman's favorite cartoon), and "Poppyseed Avenue" (a parody of Sesame Street).
Mr. and Mrs. Turner meet Tootie in the parking lot of the Dimmadelphia Cable building. She is disguised in a fedora and gray coat. Tootie shows the Turner parents photographs of Vicky's misdeeds, including the ones they had blamed on Timmy.
She also explains to them the meaning of Chip Skylark's song Icky Vicky, which Mr. Turner previously thought was about pumpkins and for the first time, Mr. and Mrs. Turner learn that Timmy was right about Vicky being an evil babysitter. Before they can thank Deep Toot for her help, she disappears without a trace. They are completely bewildered to her identity, despite her mistakenly including her real name on her cryptic notes Mr. and Mrs. Turner should find Timmy and apologize to him when they realize that he is watching TV and then Mr. and Mrs. Turner head to the Dimmadome station. In television, Timmy is about to enter the next channel, "Maho Mushi". He and his future self were riding on the credits to a show that had just ended, "Adolescent Genetically Modified Karate Cows (AGMKC)" (a parody of Teenage Mutant Ninja Turtles (TMNT)). However, Vicky zaps future Timmy's time belt, damaging it, and causing him to fade back into the future. Before he fades away, future Timmy assures his younger self that he can stop Vicky and that he is the future's only hope. After his future self was gone, Timmy becomes furious that Vicky took away the one cool adult in his life, just like she takes away everything else from him. He vows to defeat her, in Maho Mushi, once and for all.
Timmy and Vicky enter Maho Mushi and appear in a fighting arena. The use the power of their remotes to battle each other, control giant fighting robots resembling Optimus Prime and Megatron from Transformers to battle each other, fire blasts from the remote, and use the remotes as glowing swords resembling Lightsabers from the Star Wars films to attack each other. Battling to a stalemate, Timmy realizes the only way to defeat Vicky is to become old enough that Cosmo and Wanda's magic goes away, and the remotes will stop working. He ages himself all the way to age eighteen, he is happy to know that he keeps his fairies for another eight years. However, once he hits age eighteen the Fairy Taxi arrives to take Cosmo and Wanda away. The fairies resist, so a tractor beam begins to suck them toward the taxi. Before it can get them both, Cosmo manages to poof Timmy back to a kid, but he goes too far and turns Timmy back into a baby. Wanda corrects the mistake and makes Timmy 10 years old again, so he gets to keep his fairies, and the magic remotes have ran out of power so Vicky can no longer harm them. Timmy gets both of the remotes back and recharges their power, using them to blast Vicky out of television and back into her room. She lands roughly in her bed, thinking it was all a dream, when a Timmy doll with a message from Deep Toot comes crashing through her window, telling her to call the Turners because she was in big trouble. Vicky curses the name of Deep Toot, oblivious that it is really her little sister.
Back home, the Turners' plead Doug Dimmadome for his help using the cable station to broadcast a message to Timmy, because they were sure that wherever he was, he was in front of a TV. As Doug Dimmadome debates with himself whether to help the Turners' or have security remove them (since Timmy has both helped and foiled Doug Dimmadome in the past), the Turners' sneak by him and use the studio cameras to broadcast a message on TV, apologizing to Timmy for not believing that Vicky is evil, who sees the message while he is surfing through the TV world and decides that it is time to return home. When his parents finish the broadcast, he appears out of the TV, hugs them, reconcile, and then Mrs. Turner asked Doug how can they ever him and Doug calls security to have the Turners kicked out of the cable station, but Doug happly thinks what Timmy helped him in the past, makes Doug feel happy for himself. Back at the Turner household, Mr. and Mrs. Turner are furious at Vicky for lying to them, blaming it on Timmy for which he didn't do and being a mean terrible babysitter, Vicky cries and blames television for her wicked ways but his parents aren't falling for that again when they realize they cannot trust Vicky to torture Timmy and therefore, They can't trust Vicky to babysit Timmy at all and so, Mr. and Mrs. Turner fire Vicky and forbade her to babysit Timmy again. However, when it was all said an done, Timmy used the remote to pause everything, and then wished the remotes never existed, and nobody to remember all of this happened. This is because Timmy realizes that without Vicky around to make him more miserable, he would lose his godparents. He wishes the magic remotes didn't exist and that everyone forgot all the events that happened over the course of his adventure. The wish is granted, and a wave of magic erased everything that happened including Vicky's firing, Tootie's evidence against Vicky and her, Chester, and A.J.'s memories of the event. Mr. Crocker is also affected, he has finally stopped believing in fairies after staying at a mental hospital. He vows to use his mind to help the world, and he had already just invented cold fusion to capture them and said there was no limit to the good he could do for humanity. However, when the effects of the erase wish hit him, Crocker reverted back to his normal ways, believing that him about to help people was the work of fairies. He laughs crazily before he runs right back into the mental hospital.
With everything peaceful and back to normal, Timmy decides to bury a time capsule, which includes a photograph of Timmy and his goldfish. He buries it next to a flower and a tree, and tells Cosmo and Wanda about when he grows up, he will not make the same mistakes that his parents made. Wanda says that its a beautiful day out and there is so much to do outside, but Timmy and Cosmo would rather go inside and watch television, and Wanda joins Timmy and Cosmo to watch television. The scene fades to twenty years later.
The future has changed and Dimmsdale is a normal, technologically advanced place. Timmy's children, Tommy and Tammy, are unearthing a time capsule next to the tree and flower (which has grown into a bush). His son closely resembles him, while his daughter has the same glasses as Tootie and the same headband as Trixie Tang, enigmatically suggesting to the viewer their mom could be either one (The Fairly Odd Movie's official website later confirmed it is Tootie). The children take the time capsule to their father Timmy, who is now a working man at the age of 30, dressed in a tie and getting ready for work. His children ask what the time capsule is, and Timmy takes the photograph out of the time capsule. The picture of him at age 10 is shown, but the goldfish in the background are indistinguishable from normal ones. Timmy pockets the picture and leaves for work, leaving his children under the care of a violent babysitter robot modeled after Vicky. His children beg for him to take them with him, when it's revealed that Cosmo and Wanda are watching over them as goldfish like they did for Timmy 20 years ago, they remark that some things never change. The screen closes on Cosmo trying to say "Thhh-That's all folks!", much like Porky Pig from Looney Tunes in a square bulleyes instead of a round bulleyes. Then Wanda appears and asks, "Cosmo, what's the matter with you?" and Cosmo says, "Nothing. It's just really cold in here!" while freezing himself. Then Wanda glances at the camera in a weird expression.