Well, you could write a fanfiction where the TMNT are accidentally transported to the world of Pokemon. They start to explore this new world and meet different Pokemon species. Meanwhile, the Powerpuff Girls are on a mission to find a missing ingredient that can only be found in the TMNT's world. Their paths cross in the Pokemon world. They all have to work together, with the Turtles' combat skills, the Powerpuff Girls' superpowers, and the Pokemon's unique abilities to overcome various challenges like an evil team of Pokemon thieves who want to use the special ingredient for their own bad purposes.
A possible fanfiction concept could be that a powerful villain is using a combination of mutagen (from TMNT) and some dark Pokemon powers to create chaos. The Teenage Mutant Ninja Turtles, realizing they can't handle this alone, seek help. They find the Powerpuff Girls, who are also intrigued by this new threat. Together, they enter the Pokemon world to find a legendary Pokemon that can counter the villain's powers. Along the journey, they each learn about the others' worlds and abilities. The Turtles teach the Powerpuff Girls some ninja moves, and the Powerpuff Girls show the Turtles how to use their superpowers more effectively in combat situations.
To start writing this fanfiction, begin by researching the three universes. Know the abilities and backstories of the TMNT, the different types and characteristics of Pokemon, and the origin and powers of the Powerpuff Girls. Next, choose a main conflict. It could be a powerful enemy that threatens all three worlds. For example, an evil scientist who wants to use the powers of the Turtles, the Pokemon, and the Powerpuff Girls for his own gain. After that, introduce your characters. You could start with the Turtles going about their normal day in New York when suddenly a Pokemon appears out of nowhere, which then leads them to discover the existence of the Powerpuff Girls.
One idea could be a story where the Powerpuff Girls (PPG) and the Rowdyruff Boys (RRB) have to team up to face a new supervillain that neither of them can defeat alone. This would force them to put aside their differences and use their combined powers.
One idea could be a crossover where Batman and the Turtles team up to take on a common enemy like the Foot Clan and some of Batman's rogues gallery working together. Maybe they meet in Gotham City and have to adapt to each other's fighting styles.
One idea could be a story where Blossom and Brick are forced to team up against a new, powerful villain that neither their respective teams can handle alone. They start off bickering but gradually learn to respect each other's strengths.
One idea could be that the Turtles from 2003 get transported to the 2012 universe and they have to deal with the different versions of their enemies. For example, the Shredder in the 2012 version might have some new powers or tactics that the 2003 Turtles aren't used to.
Another aspect could be the challenges they face during pregnancy in terms of their ninja training and duties. Maybe they have to find new ways to stay in shape and maintain their combat skills while carrying a baby.
A possible plot is that an ancient evil that was sealed away in the 2003 universe is accidentally awakened by the arrival of the 2012 turtles. The 2003 turtles initially blame the 2012 ones but then realize they need to work together. They combine their strengths, with the 2012 turtles' modern thinking and the 2003 turtles' deep knowledge of ancient ninja lore, to defeat the evil.
One idea could be that the Turtles from 1987 end up in the 2003 universe and have to adapt to the darker and more serious tone. They could team up with the 2003 Turtles to fight a common enemy like the Shredder. The 1987 Turtles' more light - hearted and comical ways might initially clash with the 2003 Turtles' brooding nature, but they eventually learn from each other.
One plot idea could be that the gender - bent Powerpuff Girls and Rowdyruff Boys are in a school setting. The girls, now boys, are trying to fit into a more male - dominated sports team while facing challenges from the gender - bent Rowdyruff Boys, who are used to being the toughest in that area. Another idea is a story where they all live in a reversed gender society. The former PPG, now boys, have to deal with different expectations of masculinity and the former RRB, now girls, are exploring new - found femininity in a world that doesn't quite understand them yet.
One idea could be exploring the relationship between the lone rat and the cubs in more depth. Maybe show how the lone rat teaches the cubs survival skills.