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.
Another interesting fanfiction concept could be a story where the Turtles end up in Gotham by accident. They then get mistaken for some new kind of villains at first. Batman investigates and eventually realizes they are allies. They could then exchange knowledge about their respective worlds, like the Turtles teaching Batman some of their ninja techniques and Batman showing them some of his high - tech gadgets.
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.
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.
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.
Another idea might be that one Batman is from the future and has come back to meet his past self. The future Batman could show the past version some new technologies and tactics, but also warn him about the potential consequences of certain actions. This could lead to self - reflection for the past Batman and a change in his approach to crime - fighting.
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.
A possible plot for tmnt baby sister fanfiction is that the baby sister finds an ancient artifact that has a connection to the turtles' heritage. This artifact might give her some new abilities or put her in danger as various forces try to take it from her. Maybe she befriends a stray animal that turns out to have some kind of magical or otherworldly connection. The turtles are initially skeptical but then realize that the animal is actually helpful. Additionally, the baby sister could get involved in a school project about mutants which leads to some unexpected revelations about her brothers and their place in the world.
One idea could be an OC who is a new mutant in the city. They could have a unique power like the ability to control plants. At first, they are scared and confused about their new form and powers, but as the story progresses, they learn to use it for good and join the turtles in their fight against the bad guys.
One idea could be that as a girl, Leo has to face different challenges in leading the team. Maybe she has to deal with more doubts from others at first because she's female. But she overcomes them with her skills and determination.