What's the overall story of TMNT?
 

I'd say:

Life and family.

I x2 that!

In a nutshell.

Blood ties, family (and family obligation).

It begins with a circle of vengeance between families, the Orokus and the Hamatos -- Saki avenges Nagi with Yoshi; Splinter avenges Yoshi by training the TMNT to kill Saki; the Foot go round and round with the TMNT trying to avenge their father...

That's how it begins. Eventually it becomes more intimate... just the four Turtles growing older, all debts squared away but now they're drifting apart (maybe not even realizing it)... forgetting those same family ties that were the crux of everything they were about in the beginning. But still about family.