Jimmy Neutron is just like any other kid...well any other kid that is a genius.
Jimmy Neutron: Jet Fusion puts you (as Jimmy) in Retroville on a mission to free the action hero Jet Fusion. Why you? Well because it is your fault he is trapped, but Jet doesn't know that.
Retroville has undergone a horrific change because one of Jimmy's inventions has gone awry (yes, again). After attempting to make a holographic projector for a book report, a glitch in the system causes all of the settings and creatures from the book to come alive and take over Jimmy's hometown.
Now you and your faithful robotic dog, Goddard, must go through an Asian village, the deepest jungle and many more locations in order to collect the three golden idols and stop the evil Dr. Calamitous from completing his master plan (even though the evil doctor never completes anything anyway). As you travel through the levels you will end up facing your friends in battle (who have also been transformed by the ill-fated-invention).
You will end up facing Sheen as the Ultra Ninja Lord and Ms. Fowl as a Goddess of Fire, as well as Cindy (the Leviathan Queen - sort of fitting isn't it) and then finally Calamitous' most fiendish invention yet -- the Calamibot.
Along the way you will also pick up various items that will help Jimmy either build new weapons or inventions (that actually work - well, for the most part) in order to get past otherwise impossible obstacles.
Other items you need to be on the look out for are Navchips, which allow you to move on to the next level); Purple Flurp, basically the health; and White candies (collect these to unlock images in the gallery). You can also find several other goodies that will either help Jimmy along on his adventure or open up some unlockable at the main menu.