For many people, TMNT had many things going for it. A solid voice cast, good animation, and no attachment to any prior continuity. However, the plot and villains left a lot to be desired. I think revising the plot while keeping some elements intact would make it a lot better.
I would remove Winters and the Stone Generals from the film entirely. As neat of an idea as they were, they weren’t interesting enough to keep audiences engaged. Using the opening setup from the narration, I would loosely adapt the City at War storyline with Karai serving a similar role as she does in the comics (but with a similar twist to the 2003 show). The main villains would be the Shredder loyalists, purple dragons (including hun as a side story for Casey), and the Foot scientists.
For the main characters, I would keep Raphael’s Nightwatcher persona, but he would be using it to try and fight the factions as well as normal crooks. Leonardo would also keep his same storyline, but would come back because April would tell him how dangerous NYC has become since he left. Essentially, their conflict would be similar to city at war, with raph feeling responsible for the violence due to shredder’s absence, with Leo feeling only responsibility for his family. Leo and raph would have their confrontation like in the movie, but it would end with raph joining karai to help her take control of the foot instead of Leo being taken by the generals. They would be overwhelmed fighting the shredder loyalists , purple dragons and hun, and scientists, then the rest of the turtles, Casey and April, and splinter would come to help defeat them. Donatello and Michelangelo would be the same as they were in the movie.
Splinter would have a role similar to the movie but his heart to heart with Raphael would be replaced with Leonardo.
Casey and April’s relationship would be on the rocks due to Casey’s immaturity and his growing temper due to the increase in crime in the city. April would consider leaving to be with her sister Robin (she wouldn’t though because this movie isn’t long enough for that lol) and Casey would be lashing out on thugs. He would learn that Hun is the leader of the Purple Dragons and would go on a crusade to take him down permanently. I would loosely incorporate the “dark Casey” persona from the mirage comics and he would have the struggle of ending Hun or letting the authorities take care of him. He would let hun live and him and April would get back together at the end of the movie.
The movie would end with a truce between the turtles and karai, with Karai going back to a lab with the shredder being brought back with the worms from return to New York, setting up a sequel (that I would probably leave for the third movie to conclude that storyline).
What do y’all think? I welcome any improvements or ideas to this what if movie.