It is graduation time at Beverly High, but just as the ceremony gets underway, the entire graduating class, including Sam, Clover, and Alex, mysteriously black out. When they wake up, they are surprised to find themselves back at school.

Sam, Clover, and Alex arrive at Malibu University (or Mali-U for short) - a gorgeous school overlooking the Pacific Ocean as they prepare to begin their lives as college students. However, because they enrolled at the last minute, Sam has to room with Stacy, a sophomore, while Alex and Clover room across the hall.

As the girls look over the class catalogue for their first semester, they are delighted to find a course called “Espionage 101.” Considering that they are actual Spies, Sam, Clover and Alex decide to sign up and get an easy “A.” Once in class, the professor takes an immediate liking to the girls and commends them for their extensive knowledge of the curriculum. He even picks the girls to play the role of infiltrators in a class exercise recreating a “famous espionage” event from the past. As the girls carry out the faux mission (which involves stealing a top secret weapon which has the capacity to inflate the earth to the point of explosion) they are certain they will all get perfect grades. But what they actually end up getting is arrested. It turns out that the reenactment was a ploy by the professor to obtain a real secret weapon and have the girls take all the blame. But when the girls try to plead their case, no one believes. Can the girls break out of prison and stop the evil professor before he uses the weapon to destroy the world? In a b-story, Sam, Clover and Alex all get part-time jobs at the campus coffee shop.

Jerry informs Alex, Sam, and Clover to escort a extremely dangerous criminal to WOOHP's highest security penitentiary. The spies are a bit nervous at first, until they meet the villain. An elderly sweet, snickerdoodle-making lady by the name, "The Granny." Jerry warns the Spies to be cautious, since the Granny is the most notorious and ruthless bank robber in criminal history. Unfortunately, they fall for Granny's tricks. Can the Spies recapture her before banks everywhere are robbed? In a b-story, Clover meets Blaine - her dream guy and captain of the Mali-U beach volleyball team, who she tries to keep her spy life a secret from.

With Blaine as Clover's official boyfriend, Clover's love life is perfect. She was even convinced he was "the one." Although her love life is awesome, her spy life isn't running so smoothly. In fact, after a mission at The Groove back in Beverly Hills, where Clover gets attacked by a mysterious person, he accidentally leaves behind a small air pump for volleyballs. The pump has Mali-U's logo on it and each member of the Mali-U beach volleyball team has one - even Blaine! Will the spies find out what Blaine is really up to? In a b-story, Clover dreams about her future plans with Blaine.

With Blaine off on a top-secret mission, Clover tries to cheer herself up by doing all the things she loves to do – going to her fave members-only spa; shopping at her fave boutique; and eating at her fave veggie restaurant. Unfortunately, "Operation Self-Love" doesn't go quite as planned. Geraldine creates the holographic image of Clover and steals Sam's essay, ruin Alex's car and steals a WOOHP weapon. Sam and Alex yell at Clover. When Jerry calls, Clover is suspended from WOOHP. Clover is sad. Clover is framed and discovers it's all Geraldine's fault. Meanwhile, Blaine arrives at Geraldine's island, but he's kidnapped by Geraldine and calls Clover. Clover rescues Blaine, but she's kidnapped too. Meanwhile, Sam, Alex and Jerry learn everyone was framed by Geraldine. Sam and Alex arrives at Geraldine's island to save Clover. Clover and Blaine are rescued, but Geraldine has escaped from the island. She's defeated by the spies and Blaine. After Geraldine is arrested, Sam, Alex and Jerry apologize to Clover. Jerry hires Blaine to WOOHP and Blaine is sent to WOOHP Headquarters in Australia. Clover is sad, but she finds out she can visit Blaine on vacation. In a b-story, Clover faces a life where everything is turned upside down.

It's Greek week at Mali-U and Clover is psyched because she's going to pledge a new sorority, Phi Epsilon Phi, or PEP for short. Sam and Alex aren't too interested, especially when they discover that Mandy and her equally obnoxious cousin Mindy, whom the girls find out go to their school, are both PEP hopefuls! And the leader has a sinister plan which involves brainwashing her cronies! In a b-story, the girls each try to find a university activity to join.

When Jerry decides it's time to take a little R&R in Europe, he brings the girls with him to work out of WOOHP's European office in Paris – which is located under the Eiffel Tower. For their first Euro-mission, when a Romanian women's gymnastics team suddenly goes missing, Jerry sends the girls in to check it out. In a b-story, Alex contacts a distant relative only to find out, after participating in a few embarrassing "family customs," that she's got the wrong person.

With little happening in the world of espionage, Sam, Clover and Alex decide to take a little jaunt to the Italian countryside. They arrive at a quaint Tuscan villa that is the picture of serenity. Unfortunately, the serenity doesn't last long. In the b-story, Sam has but one wish: to visit Rome.

For their third and final Euro-mission, Sam, Clover and Alex are sent to check out the mysterious disappearances of various European fashion critics (including Beatrice Bash, editor of Fashion Slam! magazine). In a b-story, the girls are reacquainted with Guillaume, their former pool French boy… and this time they

When Sam, Clover and Alex find themselves under attack at various locations throughout Mali-U, they begin to suspect, because of the nature of the assaults, that past villains are to blame. However, when Jerry informs them that those villains are still secured in the WOOHP prison system, the girls are perplexed. It eventually becomes clear that their friend Britney is possessed from an accident involving her virtual training, causing her to change into these villains and even adopt their personalities! Can the spies rid their friend of the virtual demon that took possession of her? In a b-story, Mandy and Mindy start a smear campaign in an effort to turn everyone in the dorms against Sam, Clover and Alex, forcing the girls to go around in disguises and find evidence which can hopefully clear their names!

It's a bright, sunny day on the Mali-U campus. As Sam, Clover, Alex and Britney stroll across the quad, they suddenly hear a strange sound. "Woohp! Woohp!" To their utter shock and surprise, they look up to see a group of students doing what appears to be the officially sanctioned WOOHP workout routine! Incredulous, they ask what's going on. That's when Mandy and Mindy tell them: "Duh. It's only the latest workout craze!" When the girls tell Jerry what's going on, he's equally as surprised and concerned. In a b-story, with Britney being drafted back into the team again, Alex's jealousies return.

When Clover reads about the opening of a brand new underwater hotel off the coast of Malibu, she's totally psyched. Only when she tries to make a reservation, she's told that it's for VIPs only. Unless she's a movie star, pop singer or celebutante, she isn't welcome. Meanwhile, Jerry informs the girls (Sam, Clover, Alex and Britney) that water levels around the Earth are on the rise. He sends them to check it out. In a b-story, Alex gets over her jealousy of Britney.

Scientists make a startling discovery in the Antarctic--a Yeti-like snow creature frozen in a block of ice! Meanwhile, Jerry informs Sam, Clover and Alex that there have been reports of a strange being terrorizing a posh ski resort. When they arrive to investigate the luxurious place, they find that they aren't the only ones on the case - they meet Martin Mystery, a teenage paranormal investigator working for The Center – an organization much like WOOHP! In the b-story, Clover is annoyed because the nerds get a crush on her, Sam discovers she looks like Martin's sister, Diana, and Alex falls for Martin.

The Spies are sent to investigate strange reports of attacks on sushi restaurants! Can Clover and Alex piece together these strange clues, even with Sam leaving them in the middle of the missions? In a b-story, Sam keeps her undercover partnership a secret from Alex and Clover. And it's a personal mission: she has to track a recently-released ex-WHOOP prisoner.

Concerned about their friend, Alex and Clover decide that the only way to find out what's wrong with Sam is to spy on her! But what will happen when they find that Sam is involved in some shady activities? They find out Sam is going undercover as a villain, even teaming up with Jazz Hands (just to defeat him, of course). In a b-story, Mandy and Mindy move in to the girls' penthouse when a pipe in their dorm room breaks.

Evil mime Jazz Hands opens his own theme park: Mime World! The Spies work undercover at the theme park to discover what his plan is, but it's bigger and more terrifying than they'd expected! Can the Spies defeat Jazz Hands and his army of mimes? In a b-story, Jerry tries a new hair tonic… that causes hair to grow everywhere but on his head!

When strange attacks on students are reported all over the Mali-U campus, Jerry enlists Sam, Clover and Alex to check it out. Is it just a coincidence that all the attacks happen to athletes? In a b-story, Alex is selected to be the new Mali-U mascot… only instead of getting to wear a cute mermaid costume, she's forced to dress as a can of dolphin-safe tuna!

Clover takes a theater class at Mali-U, and pretty soon, everyone around campus starts acting freaky! Anyone who is in the play starts to act like their character both on and off of the stage. Is there something more to this than just method acting? In a b-story, Clover takes a theater class to meet artistic boys.

Jerry sends the spies on a mission where they quickly capture a ridiculous villain who created a special serum to turn him into a real-life version of Humongo Man – his favorite childhood action figure! Also, Alex goes on a date with Virgil, but when she decides that they should be "just friends" he doesn't want to give up- and accidentally stumbles upon the girls in full Spy gear! This gives him a new idea to win Alex over, but will it end up fantastic or disastrous? In a b-story, Clover and Sam vie for Employee of the month at Mali Café.

At the annual WOOHP picnic, the girls are surprised when the Most WOOHP-tastic Agent award goes to none other than… Clover, for her apprehension of Senor Starchy, an evil dry cleaner bent on "straightening out the world"! Clover is ecstatic when she hears about the perks that come with the award and it's not long before Clover lets the Spy Stardom go to her head. She begins to act superior to her spy-mates, and makes them do all the dirty work on missions because she thinks it's beneath her. Can the girls stay together as a spy team and stay friends? In a b-story, the girls hang out with Dean at the WOOHP picnic and old flames are rekindled.

It's Saturday afternoon and, after Jerry tells the girls he has no mission for them, Sam, Clover and Alex are pumped for a totally shop-tastic day at The Groove! As an added bonus, when they get there they discover that there's barely anyone shopping – which makes for easy access to all their favorite boutiques. With the exception of a few strange occurrences everything is golden. That is, until the girls try to leave, and find themselves trapped in the Groove! Can the Spies get themselves out of this situation without any help from WOOHP? In the b-story, Jerry gives the girls WOOHP coupons.

It's the holiday season but the Spies don't get a vacation. Their latest mission is to investigate an Unidentified Flying Object - right above Beverly Hills! After the Spies finish investigating, the town gets a strange weather twist in the form of a blizzard. While everyone is snowed in, the Spies race to find the culprit and stop the snow before the town is completely buried! In a b-story, the girls take part in the Mali-U Secret Santa exchange and learn that the holidays aren't about materialism.It's the holiday season but the Spies don't get a vacation. Their latest mission is to investigate an Unidentified Flying Object - right above Beverly Hills! After the Spies finish investigating, the town gets a strange weather twist in the form of a blizzard. While everyone is snowed in, the Spies race to find the culprit and stop the snow before the town is completely buried! In a b-story, the girls take part in the Mali-U Secret Santa exchange and learn that the holidays aren't about materialism.

When freaky occurrences start to happen all around Beverly Hills – filthy tornadoes, floods of sludge, and huge run-away dust bunnies - Jerry sends the spies to investigate the strange phenomenon. The girls discover that someone seems to be purposely scumming up their beloved city, but what terrible person would want to do that? The Spies track down their only clue - a feather from a feather duster, but will it be enough to save Beverly Hills before it's a complete garbage dump? In a b-story, Alex gets into trouble when she accidentally litters on campus.

It has been decided that the Spies will be replaced by robots, and the agents and Jerry are forced to retire. But when the next super-villain strikes, while the former spies are out shopping, the robot agents are taken over by evil and kidnap Jerry. When the spies go to his house to investigate, Mandy follows them and is kidnapped too.

Following the evil robot agents to England, the Spies discover that Jerry's mother is responsible for the kidnapping of Jerry, Mandy, Britney, Dean and Blaine, after accidentally being turned evil by a machine that Jerry was testing. The spies are able to use the machine to turn the humans good again, but the robots are still on a rampage and must be defeated the old-fashioned way.