The girls travel to the African Nation of Lyrobia to investigate a strange kidnapping attempt against that country’s Queen Tassara -- a kidnapping attempt with an anti-gravity ray! After Clover, who’s disguised as the Queen in order to protect her, is abducted from the palace, the girls and the real Tassara must go after her. They eventually discover that Makeda, the Queen’s jealous sister, is the kidnapper -- and she wants to keep her sister from signing a peace treaty with neighboring Kenyopia so that a twenty-year war between the two countries will continue and she (due to a deal she made with the General of Kenyopia) will become Queen. Can the girls stop Makeda and get Tassara to a peace summit in Geneva before it’s too late? In the b-story, Clover and Mandy compete for the title of Homecoming Queen.

The girls arrive at WOOHP to find that Jerry has retired. In his place is Mac Smit -- a handsome, charismatic, intelligent, cool, thirty-something who Sam develops a bit of a crush on. When strange things start to happen (the credit card Mac gave them turns evil, the car he lent them explodes) the girls deduce that someone is after Mac. As they follow clues to find out who the unseen assailant is, the girls soon discover it is Mac himself (he’s really a rogue WOOHP agent named Tim Scam). Mac’s plan is to use an Evapo-Blaster -- a device he developed when he was at WOOHP -- to dehydrate all the earth’s water. But first he must get rid of the spies -- just like he’s gotten rid of Jerry! In the b-story, the girls grow sick of the way Jerry is treating them and wish they had a new guardian.

The brains of the world's top scientists are being sucked dry by strange creatures from the ocean controlled by a former janitor who wants the world's memories in his hands! In the sub-plot, Sam saves Mandy and her hair after releasing it from a clay pot! Mandy wants to be Sam's best friend but actually cramps her style in the process!

A man is abducting the world's most intelligent people so that he can transfer their abilities into his son's brain. Also Sam gets a role in a play, which makes Clover jealous.

The girls' Hawaiian vacation is interrupted by a madman threatening to make volcanoes erupt all over the world. In the b-story, the girls get psyched up about the upcoming school dance, only to find out its theme isn't so great...

The girls become fugitives when they are duplicated by an evil genius who uses their clones to rob banks. In A-B Story, Clover and Mandy compete over a new exchange student from Texas.

The head of a modeling agency is stealing people's body parts to give her models perfect bodies. In A-B Story, Clover wants to win the ""Miss Groovy Smoothie"" beauty contest.

The girls compete in a reality game show to find out why the contestants are disappearing. Alex becomes aggravated with a new girl just released from juve when all she was trying to do was be nice to her.

A computer geek turns his mega-computer against those who have wronged him. It’s up to the spies to stop the computer before it carries out plans for mass destruction. B-story: Sam abuses her “student judge” power.

A sinister cookie manufacturer creates a highly addictive cookie which makes all who eat it severely fat. B-story: Clover won’t wear a hat that isn’t her “normal” size.

A villain with a Napoleonic complex uses his shrinking machine to bring the world down to size. B-story: Affected by the machine, Clover tries to return to normal size for her upcoming date.

The cruise ship Juliet disappears in the Mediterranean Sea. Our heroines investigate and find out that the passengers, and even Clover, have been turned into human-animal hybrids by a famous fashion designer. In a B-story, Clover tries to impress a guy with some really tall shoes.

The girls investigate the disappearance of the California State Cheerleading Champions, The Honeybees. They have to deal with homicidal (sort of) cheerleading robots and come up with their own routine as the "WHOOP-ettes". In a B-story, Mandy rivals Sam into winning the Spelling Bee.

Sam falls for a seemingly nice boy at school, only to find out that he is using her to steal a top secret invisibility serum from the military. B-story: The girls decide they aren’t spending enough time together, so they plan a spa weekend in Palm Springs.

A villain invents a device which literally captures extreme sports stars and places them into an extreme video game. B-story: Alex falls for a teen idol who turns out to be a computer-generated personality.

The spies are replaced by a trio of former spies who have come out of “retirement.” But Clover, Sam and Alex soon find out that the former spies’ intentions aren’t so benevolent. In a b-story, Clover squares off with a bully from her past who has just started at Beverly High.

A magician, believed to be dead, goes on a spree of thefts, using his magic tricks.Our girls find that there's more than one reason magicians don't reveal their secrets!

A villain is stealing kids youth using a gem to make himself and his cronies immortal. In a B-Plot, Sam enters a Youth Contest but is worried she won't win because she thinks she has one grey hair.

A disgruntled scientist is kidnapping world leaders and replacing them with animatronic robots who then ruin national landmarks by turning them into amusement park rides.

A madman plans to wipe out the evils of civilization by destroying it with a new Ice Age.

Shoppers are being abducted from a chain of stores in malls all over the world and brainwashed into becoming anti-mall terrorists.

The spies battle a villain who has abducted the top movie stars of the world to use them in his insanely realistic and dangerous action film. In a b-story, Sam is voted “Most Popular” in the school yearbook and has to deal with life in the spotlight.

Leaving off after the first part of "A Spy Is Born", the director Lumiere has kidnapped Alex! Sam and Clover must follow his clues to find her, avoiding his traps along the way.

An archeologist fakes his disappearance, then plots to use ancient magic to give himself eternal life and power. The spies, with the help of the professor's assistant, must stop him.

Noting that their boss is acting strangely, the spies discover that an evil scientist named Dr. V has taken over Jerry's brain. They end up being shrunk to micro size and put into Jerry in a micro-sub, as in the film ""Fantastic Voyage"".