The Powerpuff Girls fight Mojo Jojo after he kidnaps kindergarten students in a cage and steal their candy.
Professor Utonium, his son Ken, Blossom, the Mayor, and Ms. Bellum and Poochi find Bubbles jumping cheerfully as she is attacked by Mojo Jojo and takes them in for research.
Buttercup reluctantly joins the group. The girls are put into the same class to make them get along and they stop Mojo from hogging all the food in a restaurant.
The girls take turns being a mother figure to Ken, while Mojo plans to turn everyone into monkeys
Climbing the Walls: Professor Utonium, Mr. Mayor, Ms. Bellum and the girls inspect the tall building which will become Mayor's Tower when Mojo tries to claim it to.
Fuzzy Lumpkins: Fuzzy Lumpkins keeps driving the girls and friends away while they try to enjoy a trip to the woods. Princess Morbucks: Classmate Princess Morbucks (Himeko) is hit by the black Z-Rays and plots to outshine the Powerpuff Girls.
Blossom is given the task of being the bodyguard of her favorite TV hero, Johnny Cosmo when Mojo threatens him. The Amoeba Boys (now including a lady) attempt to become villains with little success.
A local shop owner and the Girl's friend, Annie is hit by black Z-rays turning her into the monster Sedusa! She attempts to glamour herself to win the heart of her friend Jason.
Buttercup trains a young kid named Justin to become a better soccer player. After falling in love with Ms. Bellum, Fuzzy decides to take her back to the woods.
The arrogant hairdresser Gilbert is hit by black Z-Rays and uses his power to hypnotize the customers to accept his eccentric hairstyle.
Believing Blossom, Bubbles and Buttercup are planning to show off, Princess follows them to unearth their plan. Mojo decides to steal all the cakes in the city.
Bubbles reminisces about Cody a boy she met when she was six years old, who promised to meet her again someday.
Mojo decides to teach the Amoeba Boys how to become villains. A camera thrown away by the Mayor takes out his revenge by turning New Townsville black and white.
The Gangreen Gang attempt to capture Buttercup during a big soccer match between the New Townsville Titans and the Cityville Colts.
Mojo attacks a fashion show that Blossom and Bubbles are participating in. After a customer puts too much vinegar on the soup, black Z-Rays turns the soup into Noodlehead and forces people to eat noodles 'the right way', but the Powerpuff Girls Z are too full to stop him.
The Powerpuff Girls find out why Princess Morbucks is showing off every night, costing them their sleep.
Ernie, the school newspaper's photographer, struggles to take a decent picture of the Powerpuff Girls. The Mayor's petty argument with his brother, the Principal, causes an electric wave monster to be created.
Mojo Jojo, Fuzzy Lumpkins, and the Gangreen Gang join forces to defeat the Powerpuff Girls.
A piano hit by black Z-Rays terrorizes the town after being played poorly by Mojo. In order to not let their grades slip, Ms. Keane shoots down every excuse the girls have to fight Mojo.
Mojo Jojo uses the Powerpuff Girls' DNA, his own DNA, and Chemical Z to create the Rowdyruff Boys.
A boy's rubber duck is lost and hit by a black Z-Ray, and Poochi decides to take care of it. A group of vegetables take all the vegetables into space after no one eats them.
A mysterious being sends a mummy to collect "white energy" from the Powerpuff Girls to escape from its prison.
A Comedy of Terrors: A comedian tries to win the heart of a girl whose father doesn't appreciate comedy. Beetle Battle: With the help of Buttercup, Ken trains his pet beetle to defeat his rival in a beetle fighting tournament.
In order to introduce him to new friends, Professor Utonium sends his son back to school.
The Write and the Wrong Way: Miyako's pen and eraser are infected by Him's black spores. The pen likes to cause mischief, but the eraser tries to stop him. Flower Power: Him's spores infect a lonely flower, who begins to cover the town in flora.
While the girls try to convince Ken about the existence of Santa, Mojo decides to ruin Christmas for all.
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Super Tough Girls: Him uses a manga illustrator's talent to create new monsters. Powerpuff Boys Z: Professor Utonium, Ken, and Poochie save the day when the girls are forced to stay for a test.
Him uses Princess' best friends to empower anyone they support.
Little Ken's Big Wish: Him grants Ken's wish to be bigger. Wild Moon Chase: After splitting the Moon in half, the girls are banned from flying.
The Powerpuff Girls are chosen to star in a drama...or so they think.
The Mighty Morbucks: Princess' older sister Duchess comes for a visit, with plans to outshine the Powerpuff Girls. Trading Faces: After an injury by Fuzzy, the girls end up in each other's bodies.
The Rowdyruff Boys use the Powerpuff Girls' clothes to taint their image.
The Professor Gets His Cut: Him challenges the girls to retrieve three items for him if they want to see the Utonium family again. Who is Lucas Clark?: After telling Princess she has a boyfriend, Blossom does everything she can to prevent the truth from coming out.
Buttercup falls for an older muscular guy and changes her looks and personality to appeal to him.
Hoppily Ever After: Blossom lets her emotions get the better of her when she meets a frog prince. Vamp on Campus: After mistakenly believing Jason is going out with his professor, Annie turns into her alter ego and goes on a rampage.
After failing to injure them when in their normal states, Him confronts the girls for battle.
Keane For a Break: After breaking up with her boyfriend, Ms. Keane accompanies Mojo on a trip to a hot spring. Like Giving Candy to a Baby: Him turns the Powerpuff Girls to kids.
The girls find Bubbles' childhood friend and help him overcome his problem.
The Happy Thought Blaster: Professor Utonium teaches the girls a new move to combat Him's pure evil. Nurse Curse: After hurting himself, Mojo prolongs his hospital stay when he falls in love with nurse.
Under the direction of Him, the monsters get together to defeat the Powerpuff Girls.
The girls use Professor Utonium's latest invention to time travel and discover Him's weakness.
In a final confrontation, the girls must stop Him from destroying New Townsville in a volcanic eruption.
