With exception of the #1 spot each episode afterwards is randomly listed. Also, I haven’t seen seasons 3 and 4 since they first aired so that’s why they don’t have much of a presence on my list.
1. DNA Is Thicker Than Water - Probably the most engrossing story of the series, IMO. The interactions between Leo and Dark Leo was top notch stuff.
2. Outbreak - Bishop is my favorite villain in the series so it was great to see him have so much screentime in season four. I always love learning about character’s backstories and Agent Bishop’s didn’t disappoint. The opening scene of his past was relatively short but it gave great insight why he is who he is. It also had a number of chilling moments like Bishop being probed and then probing an alien, the utility worker screaming as he’s mutated, Bishops body melting, the agents burning the mutants, and the pedestrian being attacked by the mutant pigeon. We don’t see most of those scenes in explicit detail but that makes them all the more effective.
3. Shredder Strikes Back Part Two - 15+ minutes of wall-to-wall action. The fight choreography this episode was simply amazing. I would also like to point out a certain moment where Splinter says the following to Shredder: “Attacking us with overwhelming numbers?! It is not the way of a true warrior.” Shredder is completely taken aback by Splinter’s words which I found really interesting but weird at the same time. In seasons 2 & 3 its pretty apparent that Ch’rell knows that he's evil and dishonorable but during that one scene in season one he was written as if he actually believed his actions were just. It would have been interesting to see the writers expand on that, but alas.
4. Secret Origins Part Three - Pretty much for the same reasons as above. Constant well choreographed action that had me on the edge of my seat. My favorite part was the turtles and Splinter giving Utrom Shredder his biggest beat down. I also wish we were shown more of the Mortu vs Shredder fight.
5. Fallen Angel - My favorite Purple Dragon episode. It had some great comedy and action and I wont ever forget the part where Angel knocks Casey out with a small bag of money! :lol:
6. Return to New York Part Three - Lots of epic moments in an already epic three parter. The turtles run the gauntlet and finally make it to Shredders throne room where they face off against Stockham. After that we get Splinter being kicked out the window, the turtles finally defeating the Elite Guard, and Leo beheading Shredder. This episode had some great art direction and presentation ; Leo holding up the Sword of Tengu, Shredder summoning the Elite Guard, the turtles looking at the screen after Shredder is defeated, etc.
7. The Search for Splinter Part One - I loved the parts with Raph when he rips apart the punching bag and then later when he is about to go berserk on the car thief. Other great scenes were the turtles fooling the Guardian with the fake Shredder dummy and planting a tracer on him, Mikeys remark about Don's puppet pigeon, everyone crowding around Don as his controls the robot cam, and Casey acting like a lunatic over a toaster.
8.Way of Invisibility - Casey being an unwelcome guest, Raph’s “ yo momma” to Hun, the Foot Tech Ninja fights, all awesome stuff.
Wedding Bells and Bytes - Great finale. We get to see Casey and April tie the knot and the turtles and all their allies defeat the Shredder and his army.
10. Lone Raph and Cub - My favorite Raphael centric episode. We usually see him co-star with Casey or his brothers so those times when he isn’t with them is a treat. His interactions with the kid were hilarious and seeing him kick the Mafia’s butts was awesome. I wish the Mob was shown more throughout the series because I felt the Foot and Purple Dragons had too much exposure at times.