So I ended up reading up on the original comics because I knew they were a bit darker than the cartoons. It seems shredder is only in volume 1 of 4. In it he’s basically a New York Yakuza boss that kills splinters master. So splinter trains the turtles to kill shredder. After that he does get resurrected once, but after that he stays dead.

Volume 2 cover a full on battle with DARPA (for experimenting on aliens and turtles), Volume 3 has a possible daughter of shredder trying to get revenge, but volume 4 retcons volume 3 and focuses on a future where aliens come to earth and the turtles can roam the streets as “aliens” (which isn’t that weird for the series as aliens first appear in volume 1).

So, yeah, it gets kinda weird.