An episode I think most people tend to over look is "I, Monster" Season 4, Episode 5. While I think "Same as it Never Was," is an incredibly solid episode, "I, Monster" directly adapts Tales of Teenage Mutant Ninja Turtles Issue #4 Vol. 1 By Jim Lawson, of the same name. Here we get the introduction of the Rat King and my god, this is probably one of the most Physically imposing Rat kings I've seen.
This episode honestly gave me nightmares as a kid, hearing Rat Kings monologue as it drips with venom along with seeing his fragmented memories with the grainy filters. It felt like I was watching a slasher flick rather than TMNT, and seeing Rat King try to pick off each of the Turtles was something to behold. The fight between Leo and Rat King was excellent, this was during the City at War arc, so Leo at this point wasn't in his right mind. To see him lose it like he did on Rat King, was equal parts awesome/frightening. Fantastic episode.