Jimmy makes a nanochip for his pants but it backfires when it gains advanced brainial capacity, and leads an attack on Retroville! Jimmy is left in plaid boxers, Sheen is left in his Ultralord underwear, Carl is left in tighty whiteys, and Cindy is left in her polka-dot panties.
In order to prove Cindy wrong, Jimmy brings Thomas Edison to the present using his Time Pincher, and ends up not being able to pry him away from Miss Fowl and Thomas Edison refuses to return to his own time.
The three friends form a rock band so they can beat their arch rivals, Cindy and Libby in the school talent show. The Boys almost beat the girls, but are undone at the last second because of their hyper-inflated egos!
Jimmy wins the honor of hosting his very own TV show, Science with Jimmy, but when the show is a flop, Cindy and Libby step and give the show a makeover. The result, to Jimmy's horror, is Funky Jam Dance Party (With Some Science).
Jimmy is hosting a sleepover with Carl and Sheen! To make it the best slumber party in history, Jimmy invents a machine to make perfect pillows for pillow fights, create made-to-order pizzas, and tell scream-your-head-off scary stories. But what happens if the invention is overloaded and the programs mix up?
Jimmy's new time-travel invention sends him and his friends back two hundred million years..
Season 2: 2003-2004
In contrast to season one, 22 minute episodes became the norm for the show compared to season one. Season two consists of only six episodes of 11 minute shows, compared to nine full 22 minute episodes.
Jimmy thinks it's cool when he's recruited by a top-secret government agency to become a spy, but what's even more thrilling is joining forces with his action-hero movie idol Jet Fusion, in an effort to save the world from Professor Calamitous and his daughter.
After accidentally scrambling Santa Claus's atoms, Jimmy must do his job of delivering presents all over the world in one night. Meanwhile, convinced Jimmy's mistake cancelled Christmas, Hugh Neutron invents a replacement holiday, Pule.
Sheen gains an IQ and gets the highest score on a math test in his class, after Jimmy uses his Brain Drain helmet to make him smarter. Sheen then gains Godly powers and plots to destroy all of Retroville.
To get out of doing chores, Jimmy creates six different clones of himself so he can go into outer space. But the only thing the clones do right is cause trouble. Jimmy rounds up all the clones and explains everything, but...he's missing one.
After being zapped in the Van Patten Radiator Belt, Jimmy and his friends get mutant powers. When the army locks Jimmy's friends up, Jimmy becomes so fed up with Cindy's insults that he transforms into a hulking monster.
Jimmy and his friends travel to a bad future where Libby is the dictator of the world! So Jimmy and his friends have to get back the gift they gave to Libby for her birthday, before she becomes dictator of the world in the future.
The boys travel to the Bahama Quadrangle, to disprove the myth of the disappearances associated with the mysterious site. Their search brings them to the secret underwater laboratory of the insane genius Dr. Moist, who has been abducting unsuspecting travelers and turning them into Algae Men.
There was supposed to be a season four, but DNA Productions had gone out of business due to the failure of The Ant Bully and production costs before any episodes could be produced. Cancelling Jimmy Neutron was a big loss for the company. There are four scripts finalized, but two of them are in secret until further notice. The fourth season was going to be darker and more serious than the other three. The season premiere episode, "Deep Impacts" would have featured the return of Evil Jimmy. Another episode, "Three's a Crowd" would have been about Cindy, Libby and Betty getting trapped in Jimmy's lab and having to work together to get out. Nick was also set to rejoin the main gang and there would've been more appearances from the League of Villains. It was thought of that the series, in terms of year runs, would've been the third longest running Nicktoon series behind SpongeBob SquarePants and The Fairly OddParents, but the closure of DNA Productions prevented this from doing so.