I think Donatello would be a great character to focus on. The 2003 Donatello is very intelligent and good at creating inventions. The 2012 Donatello is also a tech - genius. They could collaborate on some super - advanced gadget for the crossover. They might also have different ways of approaching problems due to the differences in their universes.
Raphael could be really interesting. In the 2003 version, he is hot - tempered and tough. In the 2012 version, he also has a strong personality. Seeing how he reacts to his counterpart and how they might either clash or bond could be a great focus. Maybe they have a friendly rivalry as they compare their fighting skills.
The Shredder could be a very interesting character to center on. His motives and methods are different in the 2003 and 2012 universes. If there is a crossover, it could be about how he adapts to the new situation, or how the two different versions of the Turtles deal with the two different versions of him. Maybe he could form an alliance with his other - self from the different universe to take on the Turtles together.
Definitely the interactions between the two versions of Leonardo. The 2012 Leo is more light - hearted in some ways compared to the very serious 2003 Leo. They could have some great moments of leadership clashes and then learning from each other. For example, the 2003 Leo could teach the 2012 Leo some of his more stoic leadership techniques.
I think Leonardo and Papyrus would make an interesting pairing. Leonardo's leadership and discipline could contrast with Papyrus' more naive and enthusiastic nature. They could learn from each other, like Leonardo teaching Papyrus some ninja moves, and Papyrus showing Leonardo how to have more fun. Another great pairing could be Donatello and Alphys. They are both the 'tech - smart' characters in their respective universes. They could collaborate on some crazy inventions that combine Undertale technology and Turtle - made gadgets.
Chiaki Nanami could be an excellent choice. She is the Ultimate Gamer, so if you cross her with a digital or virtual world, there are so many possibilities. She could use her gaming skills to navigate through a new digital realm, like a Matrix - like world. Her calm and intelligent nature would also make her a great character to lead the group in a crossover situation. She could figure out the rules of the new world quickly and help the others adapt.
Ross could be really interesting. Since he's an archaeologist, in a crossover with a show like 'Indiana Jones' (in a fanfiction sense), he could go on an adventure with Indiana Jones. Ross would bring his academic knowledge while Indy would have the practical experience. Their interactions would be filled with Ross trying to over - analyze everything and Indy just wanting to get the job done.
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 really interesting character pairing could be Fitz - Simmons and the TMNT as a whole. Fitz - Simmons are brilliant scientists, and the turtles are a scientific anomaly. They could study the turtles and their mutagenic origin. The turtles could also benefit from Fitz - Simmons' knowledge of advanced technology. Another pairing that would be cool is Agent Ward (assuming he's not evil in this fanfiction) and Leonardo. Ward is a skilled agent, and Leonardo is a skilled ninja. They could exchange fighting and survival skills, and their different perspectives on loyalty and duty could lead to some interesting story arcs.
Danny and Leonardo would be really interesting. Leo's leadership skills could clash or complement Danny's more impulsive heroics. Also, Donatello and Danny could have some great exchanges as Donnie is into technology and Danny has his high - tech Fenton gear. They could compare notes on their gadgets.
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 possible plot could be that the Teenage Mutant Ninja Turtles somehow end up in the Freddy Fazbear's Pizza place. Maybe they are investigating some strange disappearances that are rumored to be related to the animatronics. They could use their ninja skills to navigate the dark hallways and face off against the haunted animatronics. The turtles' unique personalities would add a fun dynamic, like Mikey being scared at first but then finding the whole situation exciting, while Raph is ready to fight from the start.
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.