Bart Simpson: Boy Genius is a JV46ship movie spoof of Jimmy Neutron: Boy Genius from 2001.
The movie begins at an Air Force base somewhere in Colorado. The base's radar detects an incoming UFO, and they send fighter jets up to examine the situation. The pilots are surprised to find that it is a rocket carrying two boys and a robotic dog: Bart Simpson, Milhouse Van Houten and K-9. Bart needs to launch a communications satellite (which is really a toaster) to communicate with an alien species who sent him a message that was garbled in the ionosphere. Unfortunately, the pulse rockets fail, and the rocket cannot leave the atmosphere. Bart tapes some soda to the toaster and throws it, propelling the soda into space. Then, the rocket falls down to town and lands on his roof. He is reprimanded by his parents. He then gets ready for school, but his antics caused him to miss the bus.
He tests his latest invention, a form of bubble transportation, made from a special bubble gum. He catches up with the school bus, but the bubble pops when it hits a tree. In the classroom, Lisa Simpson, Bart's sister, is giving a report on dinosaurs.
When Lisa says that girl dinosaurs are better than boy dinosaurs, Bart proceeds to correct her with technical data. During show and tell, Bart shows Edna Krabappel and the class a shrink ray. He attempts to shrink Lisa's head, but the ray malfunctions and does not work, however upon leaving class, the shrink ray suddenly shrinks Edna Krabappel, causing her to get tiny and end up battling a worm that has gotten out of an Apple. When walking home, Bart, Milhouse and their friend Martin Prince spot a poster for an amusement park. Martin gets excited about meeting Radio Active Man. Milhouse gets excited to touch a llama. However, their parents refuse to let them go due to a school night, and Bart is grounded, so they sneak out without their parents knowing. They have lots of fun. Bart, Milhouse and Martin both go on many rides. Milhouse and Bart go on a tramway while Martin goes to meet Radio Active Man, which is really a guy in a costume. Milhouse touches a Llama, and gets a button that says "I touched a llama" They then go on a roller coaster ride that the cars look like bats. By now, the shrink ray is working again, so Richard also had the Golden Rule.
Meanwhile, the toaster is found by a tentacled alien race. They seem to be green and they see with one eye. They fly spaceships in space. Kang and his assistant, Kodos, watch the message, Then, all the ships in the armada head to Earth. When Bart runs away, Lisa and her best friend Allison Taylor are doing Tai-Chi while Lisa drinks a soda called "Buzz Cola". Meanwhile, Bart, Martin and Milhouse went to Krustyland and have fun. The tentacled aliens take all the parents and made fake notes on the refrigerators.
On the way home, Milhouse spots a shooting star, so he, Bart, and Martin wish for no more parents so they could have fun all the time and be free. The next morning, Bart spots the Note set and reads it. The notes are the same for everyone, so Bart has K-9 scan for adult life forms. When the report comes back (none within radar range), the kids start celebrating and doing things they couldn't do normally.
The next morning, the craze has worn off, and at home, Bart is upset that his parents didn't say goodbye. Bart goes to his lab and compares the note the tentacled aliens left with notes his parents wrote. When the writing doesn't compare, Bart realizes that the notes are fake. K-9 finds evidence of aliens on the computer, and Bart tracks them to another system. He organizes the other kids in town to build rockets from the theme park rides to travel there.
While staying on an asteroid, everyone recalls what their parents did at bedtime before they were abducted by aliens. The next day, Bart, Lisa, Allison, Milhouse and Martin went to the tentacled aliens' home Planet. They met Kang and Kodos. The others saw Richard, Janey Powell, Lewis Clark and the other kids. Allison asks Kang that what does he want with their parents. Kang tells her that it's what King Ghidorah wants. Lisa asks him what King Ghidorah is. He gets tried of answering it. K-9 assaults Kang. Bart calls K-9 on Allison's cell phone and tricks Kodos into thinking K-9 will self-destruct in an explosion covering 30 square miles. K-9 frees the kids using a glitch in his obedience program (when told to play dead, he detonates in a small explosion, which blows down the door), and they make it to the arena were the parents will be sacrificed to King Ghidorah. When they reach it, an unusual ceremony is finishing, and King Ghidorah, a gigantic three-headed space dragon, hatching from his egg. Bart quickly comes up with a plan: Martin heads to an airfield to obtain a transport, he gets the mind controller, and the rest of the kids keep the guards busy.
They escape, but Kang follows them in his ship at the head of the tentacled alien fleet. He orders the ships to open fire. During the battle, Bart skims the surface of tentacled aliens' sun, and flares destroy all but Kang's ship. Kang sends a taunting message to Bart, who flies out with K-9. He uses his shrink ray to make himself the size of a planet, and blows the ship into an oncoming asteroid. Kang vows he'll be back. The kids are reunited with their parents, and they make it home without further incident. After which they had eggs for breakfast and Marge and Homer Simpson take a few sips of Bart's experimental soda and begin to burp uncontrollably. Realizing a picture of an atom (Bart's signature logo that could only be found on the front of his shirt), Marge yells "BART JOJO SIM--" before burping loudly. They all laugh and outside K-9 imitates a bird.
- Jimmy Neutron - Bart Simpson (The Simpsons)
- Goddard - K-9 (Doctor Who)
- Carl Wheezer - Milhouse Van Houten (The Simpsons)
- Sheen Estevez - Martin Prince (The Simpsons)
- Cindy Vortex - Lisa Simpson (The Simpsons)
- Libby Folfax - Allison Taylor (The Simpsons)
- Nick Dean - Richard (The Simpsons)
- Judy Neutron - Marge Simpson (The Simpsons)
- Hugh Neutron - Homer Simpson (The Simpsons)
- Ms. Fowl - Edna Krabappel (The Simpsons)
- Ultra Lord - Radio Active Man (The Simpsons)
- King Goobot - Kang (The Simpsons)
- Ooblar - Kodos (The Simpsons)
- Poultra - King Ghidorah (Ghidorah, the Three-Headed Monster)