This one picks up right where Episode I left off, and follows the reuniting of the heroes all the way up to the fight with Shredder.
Be sure to watch Episode I after this if you haven't seen it before.
Some new things I did with this one...
-A more diverse soundtrack (borrowed from Pheonix Wright 2, Suikoden 2, Final Fantasy 4, Lufia 2, Valkyrie Profile, Suikoden 2 again, in that order)
-2 new protagonists,
-1 new Major adversary introduced, more in depth in Episode III
-More dialogue to balance the movie out
I think the only improvements I can make from here are graphical improvements to make the movies better. But you be the judge on that one.
Edit 7/10/08 : Thanks for the support, #3 is turning out pretty well so far, and I hope to make some good progress while I'm out of town. Hmm, I'm aware I may have put too much dialogue in this one, a problem that I fixed in the next. I'm about 40% through with #3, so I expect to be done in maybe a week or so, depending how it goes. If you have a suggestion make sure to mention it, because most of my improvements come from feedback.