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 title is a parody of the 1973 song "Stuck in the Middle with You" by Stealers Wheel.

When Jerry sends the girls to investigate the destruction of power plants around the globe, the girls are saved by Pam, Alice and Crimson, three former WOOHP spies who were thought to be dead for seven years. While on a mission to save a hydroelectric plant, the elder spies do nothing to save Sam, Alex and Clover from a watery grave. The girls survive and soon learn that the older spies are under the control of evil mastermind Edison, who plans to extort the world for the exclusive use of solar power. Can the girls stop Edison and free their older counterparts? In the subplot, Clover meets Robbie Guthrie, a schoolmate who used to prank her a lot in elementary school, and plans to use her date to get revenge, but ponders whether he has changed his bullying ways.

• The title is a parody of the Mad Magazine comic Spy vs Spy by Antonio Prohias.

The spies are called in when the two highest-grossing actors in Hollywood are kidnapped in broad daylight. While undercover to protect the 3rd-highest-grossing celebrity, the culprit somehow manages to sneak away with an old camera as the girls' only clue. That night, Alex goes undercover as the 4th-highest-grossing actress, she is kidnapped and Sam and Clover are instantly frozen. Jerry unfreezes them and reveals that the kidnapper is a wannabe movie director named Marco Lumière and follows Alex's com-powder to a remote island. On the island, Lumière reveals his plot to create his own movie masterpiece using the kidnapped actors and actresses by putting them through deadly traps and "special effects", all of them real. Sam, Clover and Alex, however quickly save the stars and capture Lumière with his own trick. Although the mission is successful, Lumière unfreezes and escapes into the ocean. The next morning, Alex does not show up at school, with Sam and Clover receiving a message from Alex who has been kidnapped by Lumière and is now held hostage. In the subplot, Sam was voted "Most Popular Student" in the yearbook, and becomes a school celebrity.

• The story is concluded in "A Spy is Born Part II" from the second season, as Part 1 of two-part of Season 1's episode.

Psychopathic director Lumiere has kidnapped Alex and forces Sam and Clover to endure a series of deadly riddles and traps. In the subplot, Sam learns that her secret admirer's initials are A.J., only to discover him to be Arnold Jackson, the school nerd.

• Notes: This is Part 2 of the two-part Season 1's episode.

Animals at the Beijing Zoo start developing human intelligence and anthropomorphic features while humans regress into a state of animalistic retardation. The Spies ponder over how to thwart the scheme hatched by a mad scientist named Dr. Fox who has been mixing human and animal DNA. Clover falls prey to his undertaking, becoming part beagle. In the subplot, Clover must choose between joining David on a study date or attending the W.O.O.H.P. company picnic.

• This is the second time that Clover is fused with animal DNA; the first was in Episode 15 "Wild Style" when she was injected with feline DNA.

As they are at the fair, the spies are given three bracelets from an awful woman. Unfortunately, the woman who gives away the bracelets is none other than Helga Von Guggen, wearing an awful disguise. Worse still, the spies never recognized her, and she managed to lure them into her trap. As soon as they put the bracelets on their wrists, the spies suddenly pass out. When they wake up at long last, they forget everything about being spies at WOOHP, believing they are ordinary girls. Jerry goes into a fashion store, only to be captured by L.A.M.O.S., and trapped in their submarine. He hears about their evil plan, and tries to warn the girls. At school, they hear what Jerry has to say to them. Unfortunately, they do not believe in him, and they put the communicator in the trash can.

After capturing a villain called the Inventor, the girls return to find that their mothers have returned. Learning that their daughters have been spies, the mothers order their daughters to quit. Meanwhile, Mandy and her crony friends are infected by a chemical called SUDS (dropped from Alex's backpack and spilled into Mandy's hot tub) to become spy hunters or "spy-'ssassins", attacking the girls in their regular lives. The girls later try to spy on Mandy, finding the SUDS vial, but they are caught by their moms again, and are prohibited from seeing each other. It is clear now that the spy-'ssassins have posed as the girls' mothers into abducting their own daughters above all.

Having been abducted by the spy-'ssassins, the girls send Jerry a letter for help, then forced to retreat to Mandy's chalet at the Sugarflake resort, where they rescue their real moms from a runaway gondola lift. Later, they fight with the spy-'ssassins, but Jerry's arrival causes an avalanche. All three's mothers are safe, however, but the girls have seemingly sacrificed themselves to enable their mothers to escape the confusion.

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 are not 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 subplot, Clover is worried that she has become a geek magnet.

• Notes: The events of the crossover special take place after the final episode of the series.

When strange attacks on students are reported all over the Mali-U campus, Jerry enlists Sam, Clover. and Alex to check it out. The girls trace the attacks to Sigmund Smith, a guy in a bird costume who is the mascot of the rival Riptide State, who had lost to Mali-U in their previous Beach Sport Mega Tournaments. The guy has plans to knock out Mali-U's top athletes, but expands them to wrecking the entire tournament. In the subplot, Alex is selected to be the new Mali-U mascot, only instead of getting to wear a cute mermaid costume, she is forced to dress as a can of dolphin-safe tuna.

• Note: In this episode, Alex handles Sigmund Smith's neglected kitten without any allergic reaction.

When Jerry's mother accidentally ingests a concentrated dose of pure evil, she becomes evil. Going under the alias, "Mr. X", she tricks Jerry into selling WOOHP and replacing them with robots. The Spies are stupefied at the sudden turn of events, and when a crime spree begins at the mall, the robots barely react. The girls call Jerry to see what's going on, but he gets kidnapped by the robots. They follow the robots to Mrs. Lewis' house to find Jerry, their three fellow spies-Britney, Dean, Blaine- and even Mandy trapped there.

The girls investigate strange occurrences worldwide in which landmarks such as Mount Rushmore reshaped with cat faces and the Leaning Tower of Pisa is carpeted like a cat tower. The girls have a claw found at the scene analyzed, and it is made of a combination of cat and human DNA. Meanwhile, Alex finds herself turning into a catgirl. In the subplot, Clover tries to hide the fact that she is majoring in fashion design from her mother Stella, who thinks she is a premed.

• Alex has revealed that she is allergic to cats in "Wild Style"

People around the globe are mysteriously found frozen in blocks of ice, so Jerry sends the spies to investigate. As the girls follow leads to nab the perpetrator, they ultimately discover that the person behind the attacks is a wanna-be figure skater named Iceolina. Her plan is to take out the competition using her high-tech ice-skates while broadcasting her own figure skating competition where she is the only winner. Can the spies stop her before she ruins the environment and puts everyone into a deep freeze? In the subplot, Alex's father visits Mali-U to give a guest lecture.

• Note: This episode has 2 continuity errors:
  

1.) Alex's dad is of a completely different appearance than when he was briefly seen in Alex Gets Schooled
2.) Sam and Alex claim that they've never skated before despite being shown doing it in Ski Trip.

Sam, Clover, and Alex, along with the rest of Professor Plunkett's Fashion Design class, win a trip to Versailles Palace, where they will be guests at a fashion show, showcasing the outfits of Queen Marie Antoinette herself. When they get on the flight and their plane is nearly forced into the ocean as a result of Mandy's very heavy luggage, they have no choice but to get into spy mode, regardless of being told by Jerry they would not have to be doing any spying. Once they are in Versailles, things become hectic just as quickly. After the palace representative, Mr. Auguste, tells them to make themselves at home in their posh surroundings, Jerry breaks his promise and sends the girls to check out a break-in at the nearby Palais du Luxembourg. The super spies find a clue—what appears to be a missing key—as they return to Versailles and find the place under assault by a mysterious attacker.