I have figured out what the Mega Shredder will be!

[neatoman]

A Giant Enemy Crab!!!

... I'm not even joking, that's seriously what I think it is. Baxter made crustacean clones of Shredder and later on we see him with the outline of a giant crab-like creature on a monitor, what I think will happen is that Baxter turns Shredder into a giant crab as revenge for being turned into a fly.

Makes sense, if Baxter has figured out a way to become human again as (possibly) demonstrated by the recent Karai episode, he has no more reason to stick around. If he turns himself human he can safely mutate Shredder and destroy all his research and chemicals so Shredder has no hope of returning to normal. Decent revenge, don't you think?