In the Rowdyruff Boys' self-titled debut episode, Mojo created them during a stay in prison. Desperate to find a way to create a power to equal to the Powerpuff Girls, Mojo placed an anonymous phone call to Utonium, who was all too willing to tell "the stranger on the phone from Townsville Community College" his recipe for the girls' creation. Finding the ingredients of sugar, spice, and everything nice "too girlish" for his needs, Mojo wanted something "tougher" and "more manly." So he made a few variations on the recipe with everything he needed available in prison: snips (underarm hair), snails (escargot from the prison cafeteria), a puppy dog tail (pulled from the Talking Dog), and murky black slime on the prison toilet (which was considered by Mojo to be Chemical X). As with the Powerpuff Girls, the ingredients used to make the Rowdyruff Boys are based on the Nursery rhyme, "What are Little Boys Made of?", in contrast to the Girls' rhyme, "What are Little Girls Made Of?". When the Powerpuff Girls and the Rowdyruff Boys first meet, they nearly destroy all of Townsville in the ensuing fight, which ultimately concludes with the Rowdyruffs leaving the girls bruised, broken, and beaten. As the girls recover from the tears of the Townsville citizens, they are so ashamed of their defeat they consider leaving, but Ms. Bellum suggests a different way of fighting the boys, as they are naturally superior in combat. Taking her suggestion to the field, the Powerpuff Girls manage to destroy the Rowdyruff Boys with a single kiss on the cheeks, each to their counterpart. Being 10x irregular from the average boy, the kisses had 10x irregular the effect of disgust on the boys, which triggered an explosive reaction playing off of every little boy's greatest fear: Cooties/kisses from a girl, which are claimed to be able to spread. Blossom and Bubbles liked kissing, but for Buttercup, not so much.
The Rowdyruff Boys appeared in "Bought and Scold", being declared by the narrator as miscreated.
The Rowdyruff boys are seen in Divide and Conquer", on the poster as one of Townsville's wanted villains.
The Rowdyruff Boys officially reappeared in the show, in the episode "The Boys Are Back in Town," due partially to the requests by fans. They have become more powerful than before, with colors changed, and sport updated haircuts. The character HIM brought them back to life and added an anti-cootie vaccination to prevent the girls' kisses from having the prior deadly effect. The vaccination instead made the boys grow "bigger and more powerful." Unfortunately however, the girls found this out much too late and made the boys grow many times their previous size. The boys get their revenge on the girls, firstly by grossing them out in various ways (It has been said that girls can make boys uncomfortable by being affectionate towards them, alternatively, boys can make girls uncomfortable by doing gross things in front of them). Battle soon commences and the boys effortlessly defeat the girls. Soon after, Buttercup makes Butch bite his tongue and he almost cries in pain. He shrinks under his brothers' laughter and Blossom realizes that when the boys' masculinity is threatened, they shrink in size. The girls use makeup, pull down their pants and baby them so the boys shrink down to smaller than the buckles of the girls' shoes. The boys cry in shame and embarrassment, but Him soon arrives to yell at the boys for not defeating the girls and take them away. The Rowdyruff Boys have different hairstyles and slightly different personalities (sexism, male chauvinism, and misogyny to some) from their first incarnation. Unlike their first episode, the boys are not destroyed, and become regularly appearing characters in the show.
They make their third appearance in "Boy Toys," in which they are fighting the Powerpuff Girls. Then they crash into Princess' car, and Princess' questions who they are. After that, they then go back to fight the girls. As the girls are about to attack them, Princess appears and stops them. Then Princess ask the boys to be on their team, but they reject her and kick her down and they escape. The boys later appear breaking out of the burger store were about to crash the video games store until the Girls and Princess appear with their vehicles, and nearly attack them. But the boys, excited about the vehicles, smash their counterparts out of them and they play fight with each other. They become incapacitated with laughter, just as the girls had planned.
They later appear in their fourth episode "The City of Clipsville," in which the girls have flashbacks to various things (most of which were new/unaired scenes), including becoming teenagers. The Rowdyruff Boys are also teenagers in this, and despite them being known as "bad boys" (as the girls deem them), they have dulled their nature and become more slacker-ish about it. Butch even drives an Escalade, which the ditzy teenage Buttercup confuses for an escalator. Despite this, the girls all seem to have crushes on their male counterparts, and the boys likewise appear to feel the same way.
In their fifth appearance "Bubble Boy," the Powerpuff Girls kidnap Boomer after he has been ordered by Brick to steal sweets. Bubbles disguises herself as Boomer wearing his clothes and copying his hairstyle. There are several moments when Bubbles is close to letting it slip to Brick and Butch, who are still unaware that the real Boomer is held hostage, who she really is. There is even a moment when Brick looks like he suspects that Boomer is really Bubbles when he notices her panic about a cockroach. Bubbles manages to capture all of them with the containment ray, but breaks the device after showing her loogie spitting, allowing the boys to escape.
The Rowdyruff Boys appear in "Live and Let Dynamo". When the girls are trying to, figure out who is in the Dynamo.
In "Custody Battle," which would become their final appearance in the show, Mojo Jojo and Him have a major argument over which is the Rowdyruff Boys' true father and more evil parent. The boys witness several of Mojo and Him's attempts to prove their evil. In some cases they are impressed, but at the end of the episode, they are fed up, and Brick ultimately breaks up the fight by proclaiming that they only care about destroying the Powerpuff Girls, which brought tears of joy to the two villains. It is unknown what happened to the Rowdyruff Boys as they never appear again after that.
It is possible that they were simply defeated by the Powerpuffs unexplained or they just left from Townsville, and forgot all about destroying the girls, and never returned. However, it is highly unlikely that the girls would've defeated them because, in all of the boys' battle encounters with the girls, the girls were unable to defeat them.The girls relied on other methods to "beat" them such as in "The Rowdyruff Boys", when the girls flirted with them and kissed them on the cheek which destroyed the boys. Or in "Boy Toys" when the girls used Princess' plane, boat, and tank and the boys' natural love of violence against them, which resulted in the boys playing with and destroying Princess' mobile weapons. The boys had so much fun that they laughed to point where they could not move anymore and so the girls had used their knowledge of the boys to "defeat them". In "The Boys Are Back In Town", the girls embarrassed them and threatened their masculinity which caused HIM to angrily come and fetch them. In all of these fights, the boys were never actually defeated by the girls. Though if the flashback from The City of Clipsville is considered cannon, it's possible that they never left and mellowed out overtime. It should also be noted that in all of their fights against the girls, they were never exhausted or worn out.