The girls are sent to investigate the kidnappings of various military personnel and scientists by a mysterious knight. When they end up in the middle of another kidnapping, they follow the criminal through a strange portal, transporting them back to medieval England in the year 1136, 865 years ago. The knight reveals himself as a Malibu teen who wants to overthrow the benevolent king by using his modern technology, and takes Clover as his queen. It is up to Sam and Alex to stop him before the timeline is forever changed. In the subplot, the girls compete against Mandy for the best costume at the annual Halloween dance.

The girls return from an intense mission, but mess up in the subsequent school track and field meet. Jerry sends them to Hawaii to relax. Alex falls for a surfer guy named Corey, who is a research student for a volcano expert who has gone missing. After some surfing, Corey suddenly vanishes in a pile of dust, so the girls visit Iceland to consult with the scientist there. Returning to Hawaii, the girls discover that a madman called Hephaestus, a scientist whose face was disfigured by volcanic magma, is planning to make the volcanoes of the world erupt simultaneously. After failing to stop the lava in time, the girls soon learn the entire situation is just a W.O.O.H.P field test (Hephaestus is Jerry in disguise, while Corey is just a pimply guy named Morey), but they soon get pulled into a real emergency when the volcano erupts for real. The girls return in time for the school dance, but its theme is a Hawaiian luau with volcanoes.

Fed up of Jerry's butting in to their personal lives and treating them like children, the girls are happy to see the young Mac Smit takes over as the head of WOOHP. Their happiness is short-lived when Mac's generous gifts turn out to be death traps. The girls discover that Mac is actually a criminal and former employee named Tim Scam (Mac Smit is Tim's name spelled backwards), who has sent Jerry into orbit and who plans to use his inventions to vaporise the world's oceans as revenge for being fired from WOOHP.

Musician Ricky Mathis becomes an overnight sensation thanks to his song "Rock Legend." When his music causes his fans to become obsessive and destructive, three young girls named Sam, Alex, and Clover are called in to investigate the cause of this fanatical behaviour under the guise of a supporting band. While Clover is enchanted by Ricky's music, Sam and Alex investigate the recording studio and discover they are using special glowing CDs that brainwash listeners. They must stop manager Sebastian Saga from using Ricky's music to take over the world. In the subplot, Clover has a crush on schoolmate Damon Reynolds, who plays guitar and hangs out with school diva and rival Mandy.