When a few disappearances occur, the Spiez investigate. While spying in the room of one of the "victims", Tony finds adventure cards that are supposedly a special edition. The cards turn out to be clues. While walking on the street, a truck almost hits Tony, but he throws it to the other side of the road and figures out that he has super strength. When the other three Spiez are on the mission, they find out that whoever touches the cards gets the power of the character in it. In the B-story Tony wants to be stronger and taller.

Villain: Jimmy

Strange occurrences happen in the museum during the Spiez' field trip. Prehistoric creatures come alive. The Spiez investigate when they discover that an anthropologist acting like a caveman plans to return the world into the dinosaur age. The Spiez get trapped in an erupting volcano, but escape. They hurry to their hometown to finish destroying the dinosaurs and defeating the anthropologist just in time to get home before their parents arrive. In the B-story, Megan thinks that their parents are having a baby girl and is jazzed that she will not be the only girl.

When agent Britney (from Totally Spies!) disappears while investigating the disappearance of Dean, the Spiez are called in to assist the investigation and to save another spy, Blaine, from getting abducted, but they fail to rescue him. Later, Lee gets annoyed when he is put under supervision of a babysitter, although he is 13. So he sneaks out of the house and then is abducted by the same kidnapper. Their babysitter, Malinda, is really an ex-Woohp spy in disguise, and is the one who is kidnapping the agents.

Villain: Mel (Former WOOHP Spy)

Megan is teased by her brothers because she is a poor skateboarder. Then they are called for a mission to investigate strange occurrences in Dubai, involving buildings and other structures breaking down. Later, Megan goes missing after getting her new skateboard that she will use to show her brothers that she can skate. Lee, Marc and Tony find her with an army of skateboarders responsible for breaking down the buildings so they can create skateparks for themselves.

Villain: Stony Falcon (Champion Skateboarder and a parody of skateboarder Tony Hawk)

The Spiez are sent to protect a famous TV spy actor from various incidents. To keep an eye on him, the Spiez are invited to be in his Spy show, with the guidance of their parents who think they won a contest. The actor is kidnapped and the Spiez rescue him.

In the B-story, Megan is chosen to play a role in a school play instead of Tami. It goes to her head.

An experiment was stolen from a lab, and at the same time, children who are having 13th birthdays become mutated. The Spiez are sent to investigate and discover that a girl named Kat is behind it all. She was disappointed in her birthdays, so she wants to get revenge by turning other rich children into mutants during their birthdays, and therefore have the biggest party on the block.

In the B-story, Megan tries to act cool so she can be invited to Tami's birthday party so she can prove to her brothers how cool she is. Tami gets mutated, gaining wide hips and a massive butt.

The Spiez are sent to WOOHP prison to investigate the disappearance of an important chip. The missing chip contains WOOHP security codes. They find mysterious footprints that lead them to Pisa. There, the Spiez are attacked by clowns. The leader of the clowns is named the Juggler who instead of using the security codes to free prisoners, uses them to enter WOOHP Headquarters and create a crazy circus there.

In the B-story, Tony wants a date to get respect.

Villain: The Juggler

The Clark family wins a free cruise on a luxury liner. Jerry is sick and asks the Spiez to go on dangerous missions to find a cure. Someone has infiltrated WOOHP. The villain is now after the Spiez and tries to use their parents to eliminate them. The Spiez save their parents and stop the ship from crashing into an oil rig.

In the B-story, the Spiez have to retrieve remedies for Jerry's cold, but they find out it is just an allergy.

Villain: Davey Hacker (1) (Former spy candidate for WOOHP)

Someone uses a ray gun to change hi-tech modern things into ancient low-tech things. The Spiez discovered that the person is related to Boogie Gus (a villain from Totally Spies!). Without any means of communication with WOOHP, the four Spiez try to stop the madness.

In the B-story, Marc tries to find a gift for their parents' anniversary so he can earn a gift from them in return, specifically a robot.

Villain: Gus Jr. (Boogie Gus's son)

Someone has been breaking in and destroying labs of a company called Techammer. The Spiez investigate and discover that a human projectile man who loves to do stunts is destroying the Techammer labs, because the company used him and his stunts in videogames without giving him credit.

In the B-story, Lee gets braces and likes Mia, the owner of the Techammer who also has braces.

The All City Middle School Olympiad is about to have its yearly competition, but a week before the proceedings all the teams are attacked. The Spiez must find out who is responsible while protecting their school. The Spiez find out that a principal of another school is behind the attacks. His school has always placed last in the competition, so he gets back by attacking other schools and turning his athletes aggressive so they can win.

In the B-story, Lee stops being a father-like brother.

The Spiez are sent to a mission involving men from a university who are having fighting each other. They find out that the Sunrise Tan was responsible for making them act crazy over girls who have themselves tanned with Sunrise Tan. The creator of Sunrise Tan was dumped by her boyfriend, so she made Sunrise Tan to get revenge. Meanwhile, the Clark boys are acting crazy about Tami after admiring her Sunrise Tanned skin. Megan must save the day.

Villain: Zoe Quinn

The Spiez find themselves fighting against a villain who can blend into the surroundings. Tony gets captured by the villain and the older ones have to save him. The villain plans to destroy WOOHP's Core so that no one can stop him in creating a chameleon army.

In the B-story, Tami steals all of Megan's looks, which angers her.

Villain: Chameleon Leon (1)

The sibling Spiez attempt to capture a villain with no teamwork. They bicker about it and tell Jerry that they were tired of working together. So Jerry sends them into a vacation on WOOHP's ranch so that they can calm down. In the ranch, the four Spiez finally meet the original Spies: Alex, Sam and Clover (from Totally Spies) with Dean. But soon, the older spies disappear and the Spiez rescue them together, despite their quarreling. In the end, the affair turns out to be a setup by Jerry to have the Spiez work together again.

In the B-story, Tony starts to like Clover when she calls him cute.

Villain: Tex (Jerry in disguise)

Because he is a genius, Marc is promoted to WOOCSI, a new division of WOOHP that specializes in Crime Scene Investigations. Sherry, Jerry's sister, is introduced as the head of WOOCSI. Lee, Megan and Tony are sent on a mission to investigate the disappearance of intelligent celebrities. Without Marc, the three come across difficulties. It turns out that Sherry is behind the kidnappings. She drains the knowledge of the celebrities, including Marc, and uses it to get revenge on Jerry for being a goodie two-shoes brother and to take over WOOHP.

Villain: Sherry Lewis (Jerry's sister)

A library has been destroyed. Jerry sends Marc and Tony to investigate, while Lee and Megan deal with a villain destroying a museum. When Tony and Marc arrive, Tony gets hit by a beam from the villain, making him get older and taller. The spies find out that an 8-year old boy named Archibald Cranton is behind this. Tired of being a kid, he plans to destroy all the museums and libraries and turn them into playgrounds and amusement parks. The spies must take him down.

In the B-story, Tony wants to join the school choir.

Certain scientists have been abducted and the Spiez are sent to investigate. They find beeswax and a giant bee stinger. At the same time, the Spiez's snoopy aunt comes to their house and finds Megan's diary containing information about their missions. The Spiez find out that the kidnapper is a bee lady, whose DNA has combined with bee DNA. She is a colleague to the scientists she abducted.

Throughout the whole mission, the Aunt follows them and busts her niece and nephews, saying that she would tell their parents. Jerry then erases her memory about her discovery before they go home.

Certain places have reported attacks by strange creatures. The Spiez investigate and are attacked. Soon, they are led to an Animal Rescue warehouse and find out that the creatures are half-human and half-animal because their DNA was combined. It is up to the Spiez to stop these animals.

In the B-story, Tony wants a pet of his own.

Villain: Derek

Strange occurrences are happening in the seas and causeing ships to disappear. The Spiez investigate and Lee gets sucked in the whirlpool. The three remaining Spiez set off to rescue their brother and all the other people from Crabby Bob who hopes to sink the entire world into the ocean and make it safe for all fish and crabs.

In the B-story, Marc gets a crush on a girl classmate.

When strange weather patterns cause an overall rise in global temperature, the Spiez investigate. They find that the phenomena are artificial, and have been caused by the dangerous escaped villain, the Granny. The Granny's plan is to cause global warming because the years spent in the WOOHP Assisted Living Facility have caused her old bones to become brittle. It is up to the Spiez to stop the Granny and her comrades.

In the B-story, Megan becomes environmentally conscious and makes organic replacements for many everyday products. However all the products actually damage the environment.

The Spiez's mom is kidnapped by the Chameleon Leon. He turns her into a chameleon so they can work together in destroying spy organizations. Marc has to overcome his fear of heights because a spy has to be able to work at all elevations. The four Spiez must stop their mom and the Chameleon Leon before they destroy the WOOHP.

In the B-story, Marc must overcome his fear of heights, which he got from his mission against the Human Projectile (which is shown when Jerry hypnotized him).

Villain: Chameleon Leon (2)

An experimental gadget from the gadget lab called the Super Soaker Supersizer has been stolen by one of the Spiez' old enemies Davey Hacker. He uses it to kidnap Sam, Clover and Alex and then to kidnap the other Spiez to destroy them. In the B-story, Megan gets a crush on a tall new student named Paul, a transfer student from California and wants to be tall herself to have him notice her. In the end, Megan becomes a giant to beat Davey and he is taken back to WOOHP for rehabilitation. The machine malfunctions and Megan inflates. Megan and Davey shrink back to their normal sizes and Megan is past her crush on Paul, only to find he dates short girls and now wants to be shorter.

Villain: Davey Hacker (2)

An asteroid from outer space hits a space pod containing a super-villain, Alpha, who then lands on Earth. Previously, he and his twin had created clones of themselves and created chaos all around the world (Their nickname is the Chaos Twins). After Alpha and Omega capture Marc and Megan, Lee and Tony take the head of OOPSIE, another spy agency, into custody for questioning. At WOOHP headquarters they learn that their parents had originally stopped Alpha and Omega. They bring their parents in and restore their past memories. In the end all six Clarks are captured, and the four kids are sent into space. Alpha and Omega plan to use a machine to clone Cal and Karen and use the clones to wreak havoc. The kids must learn how to stop their parents and find a way to outsmart Alpha and Omega.

In the B-story Tami becomes best friends with the Clarks after they save her and her new sweater, but ends up causing more trouble for them as a friend than she ever did as an enemy.

Slick Mick tries to escape the Spiez and then is stopped by Tony and his yo-yo gadget. The public saw him stop Slick Mick and start to call him "Yo-yo Boy". Tony gets caught up in his fame. Tami becomes the president of his fan club. The Spiez are unable to stop Slick Mick again without Tony to help, as he skips out on missions frequently. The Spiez have to get Tony to forget about the fame, which he says turned out to be a 24hr job and wants to resign and stop Slick Mick from sending WOOHP HQ into the local lake.

In the B-story, Lee must get his act together after a humiliating loss of a basketball game in front of the whole school.

Villain: Slick Mick (4 times!).

Techno Tommy escapes from the WOOHP holding cell, and the Clarks are sent to capture him. After doing so Marc worries about the upcoming Science Fair Project that he is creating—a robot. After multiple failures Marc decides to borrow technology from WOOHP to help him win, but does not know the chip is from Techno Tommy. The robot and Tommy go on a rampage in the city.

Villain: Techno Tommy

Davey Hacker returns. In hopes of becoming a WOOHP spy himself, Davey follows the other spies into their home and attempts to shrink them to microscopic size. When the Spiez get shrunken themselves they must find some way to reverse the gadget and get back to their normal size before Davey smashes them into oblivion. Eventually, Davey gets shrunk and ends up going to WOOHP prison.

In the B-story, the Spiez are trying not to get caught by their nosey Aunt Trudi while their parents are away on vacation.

Villain: Davey Hacker (3)

Jerry's evil sister Sherry manages to confuse the WOOHP holding cell DNA scan because her DNA is similar to Jerry's. Once she is free she becomes an evil paparazzi with the intent of exposing Jerry and the Spiez.

In the B-story, Tami's write mean things about the SpieZ in her school newspaper column "Tami Talk" except for Lee, because Tami has a crush on him.

Villain: Sherry Lewis (2)

Absent: Karen

Weather patterns begin to go haywire and cause snow all over the world. The Spiez investigate and travel to a tropical island where they meet with Stony Falcon, who has changed from skateboarding to snowboarding. His new dream is to snowboard across the entire world, permanently changing the world's weather patterns to do so.

In the B-story, Lee gets a job at Siber Smoothie and has to create his own smoothie.

Sharky, a top real estate agent, decides to eliminate his competition by selling them his Condos. The Spiez are sent to investigate the disappearances, but find themselves facing a shark. The Spiez must stop him before he eliminates their Mom, a real estate agent.

In the B-story, Marc is excited about getting his own room in the new house (That they were going to move in but never did when they realized the Condos were a trap). Jerry decides to go through a different series of hairstyles in hopes of finding one that will suit him.

Villain: Sharky

The famous hairdresser, Tress Locksley has been repeatedly attacked. All clues led to Kat seeking revenge on her hair dresser for turning her into a hairy monster. Marc also turns into a hairy yeti during the investigation. It's up to the Spiez to stop this fight between Tress and Kat.

In the B-story, a girl named Terra Prefontaine is beating all of Lee's school records.

Mel escapes from WOOHP prison and is now out to get the Spiez by making all the adults drink juice that gives them childish behavior. Megan complains about their outdated suits and gets to try a new prototype suit.

In the B-story, Lee has to sell juice to get a new basketball uniform (not knowing he is secretly selling Mel's juice.)

Villain: Mel (2)

The Spiez investigate a stolen pair of slippers that seems to have ties to ancient ninjas. The Spiez learn another ninja figure is in their hometown, and when they arrive they learn Gus Junior has adopted the skills of the ninja making him an opponent more powerful than they could have ever imagined.

In the B-story, a new know-it-all robot, Virtual Virgil, replaces Marc as the homework helper. Marc is out to prove that Virtual Virgil does not know everything.

After finishing up a mission, the kids try to return home, only to be detained by answering a distress call from a mysterious island. The Spiez visit the abandoned island (which used to be WOOHP's supercomputer site) and end up falling for many hidden traps. Jerry must try to save the Spiez.

In the B-story, Tony hits his head during crash. This causes him to think he is a comic book superhero: Broccoli Boy.

Villain: WOOHP 123

Sebastian decides to seek revenge on WOOHP by mind-controlling the Spiez and Tami, using material from a meteor. Tami becomes Sebastian's henchman as she tries to eliminate them. The Spiez fall under Sebastian's mind-control and turn evil by taking WOOHP headquarters. Jerry again has to save WOOHP before it is destroyed.

In the B-story, Tony has terrible grades and is grounded, making him unable to go on missions.

Villain: Sebastian

Note: This villain also appeared in the first two seasons of Totally Spies! Also, first time we see all the Clarks as evil.

The Granny is back as a WOOHP villain consultant. The Clarks must go and check up on Dr. Brathwaite, to see if she is up to her old tricks. The Spiez discover she is trying to combine her DNA with plants, but this poses no threats as Brathwaite has no money to fund her research. The Spiez leave, but as soon as they are back at WOOHP must leave again to investigate the robbery of a gold reserve. The villain has a resemblance to the granny but is not her. The Spiez return to Brathwaite's house to overhear that she has made Granny young again. The Granny quickly defeats the Spiez and leaves to "re-live her youth". Brathwaite combines her DNA with the plants and tries to eat the Spiez. The Spiez defeat her and find and defeat the Granny.

In the B-story, Lee fails his French test and must have Tami as his tutor.

The Spiez are trapped in cages by a missing Austrian astronaut who crashed landed in the desert and believes that the Spiez are aliens and he is on a desert planet. Lee, Megan and Tony cause a distraction so Marc can escape and contact Jerry. The Spiez finish up and run home before their mom finds out.

The Clark boys round up a villain, but they do not let Megan help. When they return to WOOHP, Jerry tells the boys that they are contenders for "Spy of the Month", leaving out Megan. When they return home the boys are taken camping, leaving Megan behind. Feeling left out, she hacks into the open case files at WOOHP and finds a case to solve, trying to prove she is just as good as the boys. Lee, Marc and Tony are called by Jerry and told that someone has hacked into the system. Meanwhile, Megan has been trapped by a nerdy villain. The boys quickly come to Megan's aid, freeing her, and they apologize for being such jerks. They hurry off to catch the Macho Man. In the end, Megan defeats the villain, and when the Spiez return to WOOHP, Jerry announces that Megan is the Spy of the Month.

While delivering a serum to Jerry at night, the spies get tired and come late home. Trudy sees them and touches the serum, turning her into a spy-sassin. She now plans to eliminate the Spiez.

In the B-story, Marc believes in a gadget that can predict the future, but it turns out to be a keychain purchased by Jerry.

Jerry sends the spies to investigate a robotics lab, as the lab's new nano chip is missing. They find a clue: a residue. Meanwhile, Tony wants to go to the factory of the Superspy Flakes, to see how they make them, he is the last kid to receive the special ring. But when he arrives at the factory, Flaky Fructose, the owner, brainwashes him and the other winners and puts them under his control to eliminate his competition: breakfast cereal makers. Meanwhile, after learning from Jerry that the residue the found matches the ingredients in the Super Spy Flakes, Megan, Lee and Marc come to Tony's aid and take Flaky down.

In the B-story, Jerry tries to invent different spy-themed products to raise money for the agency.

One night, at WOOHP, Jerry tries to clone himself. The operation goes wrong ... The Spiez find themselves woohped by Jerry who tells them that he will retire leaving his younger clone, Jerry 2.0, at the head of the WOOHP. Their first mission is divided into two teams: Lee and Marc try to stop Termitator and Tony and Megan go to the lab to try to eliminate a crazy machine. The gadget that Jerry 2.0 gave the Spiez does not work. The Spiez then go back to WOOHP to explain everything to Jerry, but he does not want to hear anything. Jerry 2.0, who does not appreciate that the Spiez take everything seriously, decides to create clones that supposedly are "more fun". Eventually the spies manage to stop Jerry 2.0 and the clones, and Jerry decides not to retire.

In the B-story, Tony wants more acceptance from his siblings, so he decides to imitate them and copy them, which annoys Lee, Marc and Megan.

Jerry sends the spies to look for Hannigan, a comedian who destroys vegetables with a mallet. However, they find that he hasn't disappeared. The spies are then sent to protect a clown named Bizbo. Although they don't arrive in time to stop the kidnapping, they do find a clue: a piece of red rubber nose. They also discover that Funny Bone is behind it all. He has stolen the senses of humor of those who are much funnier than him, and plans to put on a successful show for an unsuspecting audience of people who rejected him to get revenge on them.

In the B-story, Megan wants to impress the captain of the school basketball team by performing in a talent show.

Several eco-activists have started to develop bizarre syndromes, among other items covered with a hard and shiny substance. When Jerry hears about this, he sends the spies to figure out the cause. They discover some strange facts about those who have been affected. In addition, it is discovered that a car wash chain called Sudstastic is the source of all of this. The own has turned one of his car washes into a test lab, and put the protesters in there to make them look weird. In a soapy battle up to their necks, the spies must defeat the washer and his crazy machine.

In the B-story, Megan decides that her family must reduce their carbon footprint.

Jerry is off to a spy conference and has put the Clark siblings in charge of WOOHP. Easier said than done! Tony accidentally orders Jerry's sister Sherry's release from prison when she was meant to be transferred! Even worse, Jerry has bumped his head while on his way to the spy conference and has lost his memory. Taking advantage of this, Sherry helps Jerry remember his spy past but tricks him into thinking the Clark siblings are bad guys. Not to mention Sherry and Jerry are now working to bust Jerry's twin brother, Terrence, out of prison. Can anyone stop them?

In the B-story, Tami is living at the Clark residence for the weekend.

Villain: Sherry(3) Terrence(1) Jerry (bumped his memory and forgot who he is)

Terrence has been freed from prison but the spiez have also escaped their deathtrap. The spiez soon learn that Sherry, Terrence, and the anesmatic Jerry are going to turn all the other spies attending the spy conference evil and must stop them as well as restore Jerry's memory

In the B-story, Tami has discovered WOOHP and is brainwashed into helping the Lewis siblings.

Villain: Sherry(3) Terrence(1) Jerry (bumped his memory and forgot who he is)

Jerry sends the spies to search for a famous chihuahua who is the face of a global taco chain. They are then sent to protect a pig named Bacon. With the help of some clues, they eventually find out that Clucky, an actor who wore a chicken costume for the company Kooky Farms for 30 years, is behind the kidnappings. He plans to get revenge on Kooky Farms for replacing him with another chicken as the mascot by controlling the kidnapped animals to regain his celebrity status.

In the B-story, Tony is convinced that he is allergic to Marc.

A mysterious space orb lands in the desert and Jerry sends the spies to investigate. After picking it up, the spies head back to school for lunch. But the orb creates an evil duplicate of Principal Shields, and turns all the students into zombies. Meanwhile, Cal has made a speech for an assembly at Southdale. He is still inside the locked school, but doesn't notice anything. Luckily, the spies manage to defeat the orb, send it to WOOHP, save the school and keep their dad from finding out their secret about being spies.

In the B-story, Tony struggles to find the goal he wants to achieve in his future for a 500-word essay.

Marc enters a contest for the company Noel Industries to design a suit. Thanks to WOOHP's engineering, he creates a suit with features such as super strength and speed, winning the competition. But he doesn't realize that Mr. Noel is actually Chameleon Leon. He tricked Marc into creating a suit that gives him back his all of his chameleon powers. He also plans to use the suit to steal gold from a train and captures Marc to use him as a sidekick. Lee, Megan and Tony must defeat the chameleon and save their brother.

In the B-story, Tony and Tami must share a two-person mascot costume after fighting over dessert at lunch.

The Spiez reminiscence about previous missions while Jerry plans a party.

Villain: Jerry (to get them to the party)

Tami starts hanging out with a strange Tami doll at school. She reveals that she has won the Sassy Lasse doll contest, making her the face of Sassy Lasse. Meanwhile, the spies are sent on a mission to investigate the disappearance of a stolen microchip. They find a clue: a paint chip. Later at school, a Tami mysteriously attacks Megan. When she and her brothers analyze the doll, they find that it matches the same microchip that was stolen. They eventually find out that Kat is behind this. She used technology to get the popular Tami dolls to attack their owners. Luckily, the spies manage to defeat her.

In the B-story, Jerry, stressed with his work, takes up yoga.

The Spiez are sent to investigate a series of abductions. They find nothing. They go to a place where a man was abducted by a tractor. They try to save him, but Lee and Tony are abducted in the process. Megan and Marc go to the Chauncy's house, where they and the Chauncy are dragged by the plants and dragged in plant vases, the plants were the head of the attacks, they get out of there and plan to defeat them. They get Lee and Tony out of the vases and defeat the plants.

In the B-story, Megan and Tami have a crush on the same boy at school and try to get his attention.