Jimmy is attempting to perfect his teleportation invention so that he may teleport to outer-space. After obtaning a Red Neutron due to Carl's misuse of Jimmy's special lens spay, he is informed that Nick is in possesion of his Area 51 map. Jimmy races Nick and wins, retriving the map and teleporting to Area 51 for his invisibility invention. Upon exiting the cave, Jimmy is abducted by a passing Yolkian ship. He easily escapes the ship via an escape pod and returns home. Sheen informs Jimmy that he is in possession of special magnets that can pick up almost anything and is willing to trade for an Ultra-Lord autograph. Jimmy complies however realizing that the Yolkians are attempting to catch him for an unknown purpose, taking Jimmy's friends instead. Jimmy aquires his rocket ship after stopping the power plant fron overheating and exploding and travels after the Yolkians. Eventually brought aboard the mother ship just outside Earth's orbit, Jimmy traverses the massive ship and reaches the fleet commander (In place of King Goobot.), threatening to shrink him. The Fleet Commander agrees to unhand his friends and return them all home.
Gameplay is relatively simple, due to the fact that the game was made with a young audience in mind. The game primarily involves reaching a certain point and completing tasks to complete the objective, allowing the player to advance to the next objective, usually by-way of Jimmy's local teleportation invention. The controls are unchangeable and use the mouse or joystick to move and pan the camera around Jimmy. The arrow keys move Jimmy and the two mouse buttons or the joystick buttons activate the invention Jimmy has equipped at the time. Upon picking up an invention, Jimmy is given the option of practicing with it. If he/she decides 'YES', the player will be taken to a virtual-world directly created for that specific invention. Pick-ups can be found in almost every 'area' ranging from burgers and other food items scattered across that particular area that can be consumed for no purpose other than to have that item collected, as well as several other items, such as flowers or candy bars, that must be brought to a specific point in that level as side quests. Serving a more direct purpose, Blue and Red neutrons can be picked up for points, and should your 'Neutron energy meter' (health bar) fall too low, Neutrons restore 'Neutron energy' (health) upon being picked up. Blue neutrons are mere collectables, whereas red neutrons are usualy harder to obtain. This is because red neutrons restore almost four-times as much health upon pick-up and award a much higher point value than their blue counterparts. At the end of the game, the player will be awarded bonus points for every Red neutron he/she collected, awarding 500 points per neutron.
- Throughout the game everyone appears to be aware of the fact that the Yolkians are present, except the Goverment agents whom continuously encircle Area 51 for evidence.
- Sheen mentions his mother in this game.
- Throughout the game, the enemies appear afraid of Jimmy even after successfully injuring him, excluding the automated cannons.
- At the end of the game, the Yolkian ships are seen leaving Earth and heading back to Yolkous. At the end, a telephone booth appears on the moon, with an estatic Jimmy standing on the suface.
- The Fleet Commander says, and-I-quote "You haven't seen the last of me Jimmy Neutron!" implying that a sequel was planned. Assuming a sequel was never released, probably due to the negative reception that this game received, there still was a sequel released, titled Jimmy Neutron vs. Jimmy Negatron.