Buttercup has always known he was different from other girls. It wasn't until he was in middle school that he actually realized what he was feeling. Soon after he researched more to make sure he wasn't just confused. He feared that what he was going through was something he was just making up in his head, and didn't want to talk to anyone till he knew for sure. At first Buttercup was fine with Blossom and Bubbles not knowing, but as he was getting older he was getting sick of people calling him a girl. He needed someone to talk to, but didn't know how to tell people. Especially since puberty was starting to hit and he was getting desperate.
That's how Buttercup started hanging out with the villains, well they were mostly retired now but whatever. He thought that at least one of them would understand, and they did. What? Just because some of them are monsters doesn't mean they're actually monsters. They might not fully understand what he's going through, but they were there for him. Shortly after he talked to the Professor about going to therapy under the excuse it was for anger management. Naturally since the Professor just wants what is best for his children, he happily obliged.
With the help of his therapist and the support of his friends, Buttercup worked up the courage to at least tell his sisters. It had been eating at him for a couple years now and he was excited and nervous to tell them. However he really should have told them sooner because he was still the person they knew and loved, just a slight change in pronouns. Bubbles hugged the life out of him upon finding out the news, claiming she always wanted a brother. Blossom smiled as she ruffled his hair and suggested they go from "The Powerpuff Girls" to "The Powerpuff's". This made Buttercup cry out of joy, this was what he wanted and more out of them. He felt silly for waiting so long, he should've held his sisters to a higher standard. Together they stood by his side instilling confidence in him as he told their father. Although the Professor was confused at first, he accepted Buttercup for who he was. Science wasn't 100% perfect and "experiments", for lack of a better word, don't always turn out as expected. The Professor soon put Buttercup on T and worked with medical experts on how to do top surgery without it affecting the chemical X in Buttercup's bloodstream.
Buttercup came out in public a short time later. Almost everyone accepted him and changed the pronouns they used, but others did think that he was just seeking attention or faking it. They even went as far as calling him a girl. He ignored those pricks and hung out with those that accepted him for him, he didn't need those types of people in his life anyway. Though that didn't stop his sisters from knocking some sense into those types of people who refused to get their heads out of their asses. Buttercup for once in his whole 15 years of existence, was finally, truly happy. His family and friends accepted him, and that was more than enough.