The formula is very valuable, it can increase a mutants stamina and make them into super mutants.
A bunch of mutant gangs are fighting to get their hands on it, and so are the humans who are against mutant equality.
My second idea is a fantasy based plot. This would also be set in an AU world with human and mutant interaction. The plot setting would be older, maybe taking place during the dark ages, but instead of a plague there is a mutagen virus or sickness that is killing humans.
Leonardo would be the adopted son of Hamato Yoshi, a well respected man that is suffering from the sickness. Leo would have to travel and find someone to help cure his father.
I red a fanfiction once with a similar idea, Donatello was a doctor of a small town, Raphael was some sort of vampire/Werewolf. How you want to portray your character is entirely up to you, depending of coarse if you're interested in a AU role play.