The film is a prequel to the television series and covers how the girls first met and shows how they became spies for the World Organization of Human Protection (WOOHP).

The film begins with three teenage girls named Samantha, Alexandra, and Clover starting their new lives in Beverly Hills, CA.

After that, Alex, Sam, and Clover introduce themselves and this starts their friendship when they later see each other again at their new school, meet the current principal Miss Skrich and their rivals, Mandy, Dominique and Caitlin.

Clover offers her new friends a change of clothes after Mandy sprays them with a chai machine, but they find themselves sucked in through a locker and into one of the offices of WOOHP.

After training, they're thrown into their first mission when famous celebrities, including rock star Rob Hearthrob and animal psychologist Peppy Wolfman, have been mysteriously abducted.

He then relates his entire plan, to abduct everyone who went through the Fabulizor and place them inside a special space station which he calls Fabutopia to live out new lives in the posh surroundings, then uses a missile to destroy all of Earth, before using his Fabulizor in reverse and give the girls each horrible makeovers (Sam gets green skin, Clover grows a unibrow and Alex gets massive pimples).

But just as he leaves, things get more difficult when Tad meets the girls again while they are still imprisoned and says he will let them fail the mission and stop Fabu himself, taking all the credit and regaining his "favorite agent" status with Jerry.

They are able to turn the missile around to destroy the station, surprising the girls since they had no idea of how to stop it earlier, and Alex whacks at the control panel with the WOOHP manual.

They then are picked up by a surprise appearance from Jerry in one of WOOHP's ships and rescue the kidnapped people from aboard the station (freeing them of the hypnotic trance by destroying Fabu's signal beacon in his staff) and evacuate safely, including Oinky, who Alex thought was never going to make it out in time, only to see him run fast to her, finally reunited with Alex before the missile explodes and destroys the station in a firework finale.

Miss Skritch had been transferred to another school in Siberia in an igloo (which has biogeographically misplaced penguins) as punishment by the Beverly Hills school district for child abuse, Fabu, Yuri and Tad are later imprisoned and set for punishment by WOOHP, and everyone who was rescued from aboard Fabu's space station have their minds erased (including Mandy).

The film aired on Disney Channel Asia on 27 February 2010, a week later that of the premiere of the season finale adaptation of its spin-off, The Amazing Spiez!.