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.
You could also write a fanfiction about the backstory of the lone rat. How did he become alone? What events in his past led him to take care of the cubs? This could add a lot of depth to the character and make the overall story more engaging.
Another idea is to create a story where the cubs face a new and dangerous threat, and the lone rat has to use all his wisdom to protect them. For example, a new mutant enemy arrives in the city. The lone rat then devises a plan to keep the cubs safe while also trying to defeat the enemy.
Another plot could be that the lone rat discovers a long - lost relative of the cubs. This relative could bring both hope and trouble. The relative might have knowledge that could help the cubs grow stronger, but also attract unwanted attention from the rat's old enemies.
The main character is obviously the lone rat. He is likely a key figure in the story, guiding and protecting the cubs.
The Shredder could be a great main villain. He's always been a big threat to the Turtles and could pose an even greater danger to the cubs and the lone rat.
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.
A great idea for Rat Patrol fanfiction is to focus on the relationships within the team. You could write about the camaraderie and how they support each other during tough times. Or, you could introduce a new character into the Rat Patrol and show how they adapt to this new addition. It could be a female mechanic who brings a fresh perspective to the group.
One idea could be that the turtles from 2012 somehow get transported to the 2018 universe. They could be really confused by the different art styles and the new gadgets the 2018 turtles have. The 2018 turtles, on the other hand, would be intrigued by the more traditional look of the 2012 turtles. This could lead to some funny moments as they try to communicate and figure out how to get the 2012 turtles back to their own universe.
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.
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.
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.
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.