An average day in Bikini Bottom turns sour for SpongeBob SquarePants when he gets sucked into a mysterious portal. Several other Nicktoons are also snatched away from their own worlds and all are soon stranded in a mysterious laboratory.
Soon, they see the being responsible for their kidnapping: Lord Nitro, who desires that the Nicktoons race through his planet solely for his amusement. Given unique vehicles and sent into racetracks based on their homeworlds, the Nicktoons compete not just for victory, but to escape from their mysterious captor.
When all six race courses are cleared, Lord Nitro will reveal its true self. Nitro then said if the Nicktoons can beat him, they will be free to go. Otherwise, they will be trapped here forever. Beating Nitro together with four other Nicktoons including the player in his race track results in Nitro stating he can't lose to those Nicktoons. The six Nicktoons said they beat him and demanded release. Nitro then replied that he isn't going to let that happen and gave them something that will go off in thirty minutes before flying off, much to the Nicktoon's surprise. Jimmy then works on the machine so that everyone can get back home safely. His actions reversed the driver extraction sequence, sending all six Nicktoons back to their own home planets. 
The following characters are playable for Nicktoons Nitro.
- SpongeBob SquarePants - Cart: Hot-Rod Boatmobile - Home World: Bikini Bottom
- Danny Phantom - Cart: Phantom Car - Home World: Ghost Zone
- Jimmy Neutron - Cart: Rocket - Home World: Retroland
- Timmy Turner - Cart: Flaming Paint Hot-Rod - Home World: Fairy World
- Zim - Cart: Voot - Home World: Irken City
- Avatar Aang - Cart: Staff - Home World: Four Nations
- Lord Nitro - Home World: Planet Nitro