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.