- King Goobot has organized the most diabolical collection of bad guys to ever assemble on one space station. Their mission: Get Jimmy Neutron.
- King Goobot from the original film sends invitations to a collection of Jimmy's previous adversaries from the past so they can join together to destroy him. These villains are; Professor Calamitous, Beautiful Gorgeous, The Junkman, Baby Eddie, Eustace Strych, Grandma Taters, Zix, Travoltron, and Tee. The villains spend most of their time squabbling amongst each other; in particular, Tee is disrespected by everyone and Beautiful Gorgeous and the Junkman can't stand each other.
Meanwhile on Earth, Jimmy, Cindy, Carl, Libby, and Sheen are in the lab. Jimmy is showing off the newly upgraded wormhole generator and wants his friends to test it for him, not caring that they'll never return home. Cindy notices a containment chamber in which Jimmy keeps his dangerous experiments which are; the love potion and the N-Men packets, which would temporarily restore their superpowers for thirty minutes. Jimmy's friends show interest in regaining their superpowers, but Jimmy warns them that the packets should only used in the case of extreme emergencies (pretty much like literal a "life or death" situation). Jimmy believes that people cannot change and that they would still use their powers with no control.
The League of Villains arrive, and, acting in teams, they disable Goddard, seal off Jimmy's lab, and incapacitate Jimmy's friends by playing music that is impossible to not dance to. Once this is done, they kidnap Jimmy with ease, because they have disabled his usual methods of defense. Unbeknownst to the villains and Jimmy, Sheen manages to sneak onto the ship before it exits Earth's orbit despite being stuck in dance position.
The villains laugh evilly at Jimmy once they abduct him and hold an unfair trial, without giving Jimmy a chance to defend himself, and declare him guilty. Sheen breaks into the courtroom in a poorly thought-out plan to rescue Jimmy, which doesn't go much further than breaking into the room. Jimmy and Sheen get taken to a prison cell, where Tee guards them, while the villains argue about what the best way to kill Jimmy is. After thinking of complicated and silly ways to get rid of Jimmy, Eddie suggests simply blasting Jimmy and Sheen into deep space and they all agree.
Meanwhile, Sheen starts making friends with Tee, even though Jimmy tells him not to. Jimmy stubbornly believes that Tee is evil and cannot change, as Jimmy said earlier about the N-Men packets. Tee warms up to Sheen because the other villains have been disrespecting him and the two become friends. Tee loans a PDA-like device to Sheen (which contains Tee's diary), which Jimmy uses to contact Carl, informing Carl about the kidnapping and what to do. Carl, following the instructions, takes Cindy and Libby to the lab, grabs the N-Men packets (unknowingly taking the Love Potion), and unknowingly drops Jimmy's packet. Cindy sees Jimmy's pictures of Betty Quinlan, which Carl quickly takes away from her. The three shoot off in Jimmy's rocket to save Jimmy and Sheen from the League of Villains. Cindy flies the rocket instead of leaving it on auto-pilot like Jimmy asked. Cindy finds another picture of Betty Quinlan on Jimmy's rocket and they almost get hit by a plane.
Jimmy's parents see the kids take off, and try to see if there's anything they can do to help. They head to Jimmy's lab (which Hugh still thinks is a disco); while there, Hugh plays around with Jimmy's wormhole generator, and accidentally sends the town back to the Cretaceous Era .
Tee, wanting to help his new friends, helps Jimmy and Sheen escape. The three of them use a small escape pod to get off the ship. The villains discover this plot, but they are too late to do anything about it. Fortunately for the villains, Carl, Libby and Cindy arrive. The villains bomb them, and they crash on Mercury and Cindy agrees to put it on autopilot next time. The villains chase after Jimmy's friends, knowing that Jimmy will turn back to help them, which is exactly what Jimmy does.
As Jimmy shows up to help his friends, the villains arrive as well. Jimmy and his friends take the N-Men packets, all except for Jimmy, who realizes he got the Love Potion. They immediately realize that the packets were mixed up, as each of them has someone else's superpowers:
Carl gets Libby's invisibility powers while Libby gets Carl's burping powers. Sheen gets Cindy's flying and super strength while Cindy gets Sheen's superspeed and poor bladder control. Because they're not used to the superpowers, they mess up the attempt to defeat the villains. The villains put them into a pit and have Junkman pick up a boulder to throw on them. Cindy, stuttering, tries to confess that she loves Jimmy. Realizing what she's saying, reminds Jimmy of the love potion, and kisses Cindy on the cheek as he runs off to save them. Jimmy blows the Love Potion at the villains, causing Beautiful Gorgeous and the Junkman to fall madly in love with each other and start making out. The gang then takes advantage of the distraction and escapes.
Jimmy, his friends and Tee think about hiding on the moon but change their minds after getting a message on the rocket monitor from the annoying Brobot, so they ride back to Retroville, only to be sucked into the wormhole that Hugh created. The League of Villains (now only Grandma Taters, Calamitous, King Goobot, Baby Eddie, Eustace, the Junkman, Beautiful Gorgeous, Zix and Travoltron) follows them into the wormhole. Jimmy tries to figure out how to reverse the wormhole while his friends use their superpowers to try to protect the townspeople from the various dinosaurs. Zix and Travoltron side with the heroes in the process after the kids rescue them. The villains show up to complicate matters.
Fortunately, Jimmy finds a way to fix the force field, but does not want the villains to return. He gets a force field generator and traps the League of Villains (excluding the Space Bandits) in the Cretacious Era, while Cindy disables the wormhole-after Jimmy promises to throw out all of his pictures of Betty Quinlan. At the end, Sam opens the Candy Bar and invites everyone in, and the Space Bandits offer to pay for the milkshakes. Jimmy takes Cindy by the hand as they walk in.
Meanwhile in the Cretacious Era, the other villains are cornered by a T-Rex and Baby Eddie drives them away with a 5-day old dirty diaper.
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