In the story, a government official is convinced Michelangelo is actually an alien (because that is clearly more plausible than being a Ninja Turtle) and injects him with truth serum. When the serum fails to get results, he decides to go the pliers route instead while video recording it like some kind of snuff film. After all, who wouldn't want to be remembered as the guy who made contact with alien life and then strapped it to a table to yank its teeth out?
We do have good news, though -- the interrogator didn't gouge out Michelangelo's eyeballs, as the cover implies. No, he's blind because a Molotov cocktail blew up in his face during a prior battle in Jerusalem (we're starting to think that all comic book plots sound like utter madness when presented out of context). Still, when Michelangelo continues to insist he is in fact a mutant turtle even in the face of grueling torture, you might think the worst is over. But that's when the official breaks out the electric cattle prod:
Mikey = Marsellus Wallace, Leo = Butch.