The plot revolves around the fact that characters from many Nickelodeon worlds have been misplaced into each other's worlds, and Jimmy Neutron has taken into his hands the job that these characters are brought back to their own worlds. He sends out Danny Phantom, Arnold, SpongeBob, Tommy, Otto, and Timmy to take photos of the misplaced characters with his new invention, the "Neutrino-Cam 4000", a camera that also functions as a teleporter, which will send them back to their own worlds.
As the player progresses, it becomes clear that Zim is the mastermind behind the whole mess, and Jimmy soon realizes that after the player has cleared all the levels. Jimmy then flies off in his rocket to Zim's ship and stops the Irken's scheme. After taking a group photo, Zim works on his NEW plan to take over the world, making the ending sequence say, TO BE CONTINUED...
In each level, the player has to meet a certain number of set points in order to progress. This is achieved by accomplishing the following missions:
Photographing a certain number of out-of-place characters Photographing something exclusive to that level (for example, "another photographer" in the Dimmsdale Elementary School stage) Photographing a certain number of in-place characters (usually six) Photographing six of a certain paraphernalia in its level (i.e. Jellyfish in Bikini Bottom) The player does not necessarily have to accomplish all of these goals, but it is recommended that they focus mainly on photographing the misplaced characters; photographing and transporting these characters is worth 1000 points each, while everything else is worth 10. However, the player gets bonus points if they clear the other objectives in addition.
Throughout the levels, the player's camera can be damaged by mechanical bolts rolling about on the ground, however the character can take a picture of it to dispose of it. If the bolt reaches the player, the characters themselves do not take damage from these (but bounce back), but ironically enough, the camera will, and should its energy meter be completely drained, it will break and Jimmy Neutron will have to repair it while the player is given the option to continue. The player will also fail a level if they are unable to reach the required goal score for that level.
At the end of each world, the character will face off with a robot boss built to resemble another character. In order to defeat the boss, the player will need to take photos of it several times, stunning them on the first camera flash and then delivering a blow with another flash. During the boss battles, the bosses will fling mechanical bolts which cause as much damage as the ones in the regular levels. Before each boss battle, the player's character and the boss will engage in a conversation that is different depending on which character the player is using (for example, Timmy will remark to the Helga robot, "Something tells me you'd make an even worse babysitter than Vicky!"); the conversation becomes a bit lengthier if the player uses a character from the same show as the character whom the robot's appearance is based on.