In order to stop an ecological disaster, Ken Kitazawa used Chemical Z, a new form of the Professor's original substance Chemical X, to destroy a giant glacier. The Chemical Z is caused by Peach's accident of dropping a Daifuku (a Japanese confection consisting of a small round mochi stuffed with sweet filling) which had dissolved in the chemical. However, the impact of Chemical Z caused several black and white lights to appear in the skies above Tokyo City. Three ordinary girls, Momoko, Miyako, and Kaoru, were engulfed in white lights and soon became the new defenders of Tokyo City: the Powerpuff Girls Z. However, the numerous black lights caused others to turn to the side of evil. And so, using their ultra super powers, Hyper-Blossom (Momoko), Rolling Bubbles (Miyako), and Powered Buttercup (Kaoru) dedicated their lives to defending Tokyo City from the likes of those swayed by the black lights and Him's black particles. Fighting the Rowdyruff boys, Sedusa, Princess, or any other, the girls are always there to help.
Powerpuff Girls to the Rescue: The Powerpuff Girls fight Mojo Jojo after he incarcerates kindergarten students and steals their candy. The Secret of the Powerpuff Girls: The origins of the Powerpuff Girls are revealed.
Professor Utonium, his son Ken, Blossom, the Mayor, and Ms. Bellum and the others find Bubbles as she is attacked by Mojo Jojo and take 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 causing more trouble.
The girls take turns being a mother figure to Ken, while Mojo plans to turn everyone into monkeys.
Mojo's Revenge: Angry with being teased at the zoo, Mojo attacks a fruit seller. Climbing the Walls: Mojo decides to move his base to the new observation tower being constructed, but the girls think otherwise.
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 is hit by the black Z-Rays and plots to outshine the Powerpuff Girls.
Mayor for a Day: Blossom is given the task of being the bodyguard of her favorite TV hero when Mojo threatens him. The Infamous Amoeba Boys: The Amoeba Boys (now including a lady) attempt to become villains.
A local shop owner, Sakurako, is hit by black Z-rays and turns into Sedusa. She attempts to glamour herself to win the heart of her friend Souichirou.
Coach Buttercup: Buttercup trains a younger kid to become a better soccer player. Fuzzy in Love: After falling in love with Ms. Bellum, Fuzzy decides to take her back to the woods.
The arrogant hairdresser Gigi is hit by black Z-Rays and uses her power to hypnotize the customers to accept her eccentric hairstyle.
Friends in High Places: Believing Blossom, Bubbles, and Buttercup are planning to show off, Himeko follows them to unearth their plan. Happy Birthday, New Townsville: Mojo decides to steal all the cakes in the city.
Bubbles reminisces about a boy she met when she was six years old, who promised to meet her again someday. His ailment is changed into a broken ankle in the English dub.
Mojo and the Amoeba Boys: Mojo decides to teach the Amoeba boys how to become villains. Revenge of Negatron: 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.
Fashion Action: Mojo attacks a fashion show that Blossom and Bubbles are participating in. The Way of the Noodle: A ramen monster tries to force everyone to eat ramen his own way.
The Powerpuff Girls find out why Himeko tries to stand out from everyone else.
Picture This: Jesse, the school newspaper's photographer, struggles to take a decent picture of the Powerpuff Girls. Revenge of Digitron: The Mayor's petty argument with his brother causes an electric wave monster to be created.
Mojo Jojo, Fuzzy Lumpkins, and the Gangreen Gang join forces to defeat the Powerpuff Girls.
Practice Makes Pandemonium: A piano hit by black Z-Rays terrorizes the town after being played poorly. Ms. Keane to the Rescue: In order to not let their grades slip, Ms. Keane shoots down every excuse the girls have to go fight Mojo.
Mojo Jojo uses the Powerpuff Girls' DNA, his own DNA, and Chemical Z to create the Rowdyruff Boys.
Quack-Quack Attack: A boy's rubber duck is lost and hit by black Z-Rays, and Poochie decides to take care of it. Veggie Vengeance: A group of vegetables take all the vegetables into space after no one eats them.
A mysterious being sends a mummy to collect 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.
Attack of the Sushi Monsters: Him's spores infect a sushi-making machine, which creates a menacing group of sushi monsters. Cat On a Hot Tin Poochie: After Princess is returned to her normal form, Sapphire stays behind and spends the night with Poochie.
Princess, Sedusa, and Violet (Lady) from the Amoeba Boys join forces to create havoc in New Townsville.
Harmed to the Teeth: Blossom and Mojo go to the dentist after eating too many sweets. Beware the Hair: The girls encounter a dancing monster when they go on a trip to a disco.
The origins of Him are revealed.
Dunga Din: An ostracized bug hit by black Z-Rays tries to impress a female bug. The Beanie Meanie: Annie becomes distracted when Jason temporarily leaves and uses her alter-ego to get him back.
A classmate of Blossom reveals his love for her.
There's No "I" in Powerpuff: Tired of not being recognized as the leader, Blossom runs away with a pasta monster who doesn't know his purpose. Keane Kong: Mojo convinces Ms. Keane to go on a date with him.
Blossom and Buttercup spend the night at Bubbles' house.
Weeding out The Monsters: A group of weeds terrorizes actresses when they aren't called by their names. The Dog Days of New Townsville: The spirit of an ancient shogun possesses the Mayor, who passes a law that allows all monsters to do what they want.
Him uses Bubbles' doll Octi to break up the team.
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.