"The Big Beginning"
Timmy makes a wish to star in his own movie trilogy. He is interrupted by Jorgen, who takes his fairy godparents away and sends Timmy home. When he gets there, Timmy's parents and school friends don't remember him, and an Eliminator appears after Timmy calls out his own name. In an alley, the Eliminator projects a space vortex through its mouth to inhale Timmy. Jorgen saves him, and the two arrive at Fairy World. Meanwhile, the fairies are hidden as gumballs inside a truck stop bar by Jorgen. After being blown into a bubble from a kid's mouth, Cosmo takes Wanda and Poof with him as he floats away. The rest of the fairies use Cosmo's method as their escape plan.
At the Cave of Destiny, Jorgen explains to Timmy the cave prophecy, where in ancient times fairy warriors, represented by stars in space, fought and eliminated The Darkness with light. The ancient fairies also hid a powerful white wand, which is to be found and possessed by the chosen one, Timmy Turner. As stars in space disappear and The Darkness approaches, Timmy arrives back on Earth and tracks his godparents down in Las Vegas, where the Middle-Aged Rock Festival is held. The M.A.R.F. features the rock band Kiss, who reveal to Timmy that they are the galactic protectors of the white wand, which is their star-shaped guitar. The Darkness and Eliminators arrive at the venue, and the fairies arrive to defeat Eliminators while Timmy defeats The Darkness with a rock solo performance on the white wand. A celebration follows at Fairy World, where Turbo Thunder appears and takes the white wand from Timmy.
"The Exciting Middle Part"
Eliminators and The Darkness invade Yugopotamia—a planet that is home to squid-like aliens called Yugopotamians—and steal "fake-i-fiers", belts that allow users to transform into anyone else. Yugopotamian prince Mark Chang goes to Earth and notifies Timmy of this, and the group discovers that there is a second part to the cave prophecy: Timmy must find the second wand, located at the Blue Moon. Timmy and Mark teleport back to Dimmsdale, only to discover Timmy's parents and friends are now Eliminators in disguise. Because his real parents and friends have been kidnapped by Eliminators, Timmy seeks help from people who hate him: Mr. Crocker, Dark Laser, and Vicky. Setting their differences aside, everyone cooperates and boards Dark Laser's death pod and depart into space. During their rest stop at planet Frigidarium, the aliens inside the cantina are Eliminators who send Timmy's enemies to the Abracatraz Prison in Fairy World. Turbo Thunder saves Timmy and Mark from the corrupting planet, and the three eventually arrive at the Blue Moon, where the rock guardian grants Timmy the second wand.
Meanwhile, Eliminators incarcerate the fairies at the Abracatraz Prison and put Timmy's friends and family in the same cell with Timmy's godparents and Jorgen. After Poof frees the group and locates the wands, Jorgen takes everyone to the Blue Moon. Timmy's friends, enemies, family, and the fairies defeat Eliminators with a combined magical attack and have a reunion with Timmy, which is interrupted when The Darkness tries to inhale him. The second wand produces no effect, and Timmy realizes he has no other choice, so he sacrifices himself into The Darkness, after sharing a kiss with his long-term crush Trixie, leaving the others to mourn.
"The Final Ending"
Timmy wakes up in what looks like his bedroom; in reality he is still inside The Darkness, and the world is merely an illusion. Timmy's fairy godparents and Jorgen come to rescue him, and they exit The Darkness successfully. Back on Earth, the Lead Eliminator uses Jorgen's wand to take Timmy's friends and family away. Military Extraterrestrial Research Facility agents launch an array of military weapons at the Eliminator, but he absorbs the ordinance and turns into a more powerful version, the Destructinator. He surrounds the Earth with a steel casing, which transforms the M.E.R.F. agents into his henchmen. They plant explosives inside Earth and give the Destructinator a detonation remote.
Timmy and his fairies return to the Blue Moon via M.E.R.F.'s escape pod to retrieve the second wand. A weakened Turbo Thunder reveals the second wand only opens underneath a secret cave, which contains magical wands and the final part of the cave prophecy: to find the ice wand. The group returns to Fairy World with the wands to free the imprisoned fairies before everyone heads back to Earth. The fairies arrive and use their magic to remove the Earth's metal casing. Timmy heads into space with the Destructinator following him; the Destructinator attacks him, which sends him back down to the Earth, at its north polar region. After Timmy tricks the Destructinator into inhaling the explosives, he reveals that he stole the detonator remote from him back in space and uses it to obliterate him.
A polar bear—the guardian of the ice wand—raises the ice wand from beneath the ocean. The fairies add an ice wand to each planet of the Solar System. Along with the white wand at Fairy World, the ice wands create a celestial smile that projects its light into The Darkness. The smile transforms it into a bright sun, The Kindness; Timmy concludes it was only looking for a friend. The group returns to Dimmsdale, where an Eliminator crashes in front of them and spews out everyone who had been sucked in. Everyone parties in Fairy World and celebrates the chosen one's accomplishment.
