Ninja Turtles Adventures #42: How Future-Raph Lost His Eye
I think this about covers the requests/suggestions I've gotten from lbd_nytetrayn. This comes from Part 1 of the Future Shark Trilogy, the first arc to feature the future-Turtles.
The future-versions of Don and Raph bring the present-day Turtles (as well as Splinter and Ninjara) to their time. Why? Read on.
The fish-guy is Jacques, AKA Merdude, who Armaggon abducted during his debut in Mighty Mutanimals #7.
Unfortunately, I don't have Part 2, which I believe explains what the heck Shredder is doing 100 years in the future. If anyone out there has it, scans would be greatly appreciated.