The Beginning of the End
 

I just finished the 87 series i never saw the red sky seasons as a kid so they were new to me

in the beginning of the end episode the bad guy dregg transformed Leonardo into a monster i guess i don't know how to describe it but im sure everyone knows what im talking about at the end the other turtles were able to cure him returning him back to normal but then the bad guy(s) who were spying on the turtles via cambot stated that although Leonardo looked normal he had permanent altered Leonardo's genetic structure and he would use it to his advantage but then 6 episodes later the series ends without another word about it

i was intrigued by this though i wonder what they were planing with this were they hinting that Leonardo could be dying or maybe turn him into a sleeper agent so to speak

Well it was the shows final season, so who knows. Maybe he would had further trouble in the future.

While it was never specifically addressed again, I always assumed that the plan Dregg was referring to at the end of "The Beginning of the End" regarding using Leonardo's permanently altered genetic structure was a part of the plan he executed in the next episode, "The Power of Three", where Dregg uses the DNA of all 4 turtles as well as Krang to enhance himself.

Dregg pumped Leonardo full of plutonium with the supposed intent of him exploding and taking the city and more with him. But the whole thing was a ploy to get the Turtles to steal chemicals from him to diffuse and stabilize Leonardo, then analyze which ones were taken so he knew how to create stable super mutagen to make him a super being. The last-second addition of Shredder and Krang was the icing on the cake that wouldn't have happened if Mung hadn't mentioned them.

Dregg's original intention wasn't to turn Leonardo or anyone into a hyper mutant. That was an unanticipated reaction to stealing a fragment of the Vortex Crystal used in the Demutation Ray. This unfortunately played to his advantage and here we are.