Leo's desperate attempts to infiltrate the Foot's lair inadvertently leads to a gargantuan threat being unleashed on New York.
- Back for the Dead: The Shredder mutants return only to be mutated into the Mega Shredder, only to be seemingly killed.
- Book Ends: The episode starts off with rain and ends with rain (of a sort).
- The Bus Came Back: The trio of Shredder mutants make a comeback, but, well, see above. Also, Donnie has repaired the Turtle Mech, last seen about a year ago. Also, the same recurring homeless man temporarily hampers the Turtles during the opening.
- Continuity Nod:
- We get to see the training room from Clash of the Mutanimals, now repaired.
- The Turtles are seeking a brain worm so they can reverse-engineer it in an effort to cure Karai, who was brainwashed in The Deadly Venom.
- The Turtle Mech is only just being repaired after being taken out of action in The Invasion.
- Once again, the Turtles (especially Leo) are going behind Splinter's back in an effort to save Karai.
- Leo dons his outfit from Vision Quest.
- Shredder threatened Bradford and Xever that he'd have Tiger Claw beat them to a pulp as punishment for further failure. Here, we see him go through with that threat when it comes to Zeck and Steranko.
- Extra Eyes / Eyes Do Not Belong There: The Mega Shredder has quite a few.
- Fusion Dance: Bebop and Rocksteady trick the Shredder mutants into hopping into Stockman's vat of mutagen, and they combine into a colossal, grotesque Kaiju.
- Game-Breaking Injury: For this episode, anyway. Raph's leg is sprained during the initial mission, sitting him out until he helps pilot the Turtle Mech.
- Genetic Abomination: The Mega Shredder, a combination of the Shredder Mutants and beastly clones of Oroku Saki.
- Kaiju: The Mega Shredder is outright called one.
- Mind Rape: Shredder has Karai hooked up to a machine with mind control worms being painfully inserted into her brain. This seems to be a regular routine. Once again, it's Splinter's fault.
- Multi-Armed and Dangerous: The Mega Shredder.
- Mythology Gag:
- The title is a reference to the second movie when Shredder mutates himself.
- This isn't the first time in the franchise a Turtle has been eaten alive and fought their way out.
- In perhaps a sign of Villain Decay beginning to take place, Bebop and Rocksteady have their first humiliating defeat that was caused by their bumbling nature.
- Never My Fault: Shredder is once again passing blame onto Splinter and the Turtles. This time for Karai being hooked up to a machine that inserts brain worms into her head, which he had her hooked up to.
- Bebop and Rocksteady blame each other for creating the Mega Shredder, and in front of Shredder they blame the turtles for it.
- Nice Job Fixing It, Villain: Bebop and Rocksteady manage to capture the Turtles, but their taunts led the duo to create a very gigantic mutant that ended up freeing the Turtles and destroying part of Shredder's lab.
- Nice Job Breaking It, Hero: this mutant then goes on a rampage throughout the city, putting the people endanger and requiring the turtles to stop it.
- No-Holds-Barred Beatdown: Tiger Claw delivers some brutal punishment on Shredder's behalf to Bebop and Rocksteady for their failure.
- Rain of Blood: When the turtles blow up the Mega Shredder, it rains green goo over the city.
- Shout-Out:
- The Mega Shredder has some Godzilla-esque dorsal fins on its back and has a similar theme play when it appears.
- The Turtle Mech battling the Mega Shredder is reminiscent of Pacific Rim.
- In a case of using Stock Sound Effects, at least twice, the Mega Shredder lets out the roars of the Indominus rex.
- Leo using the two grappling guns and two swords to fight a giant monster. Attack on Titan anyone?
- Too Many Mouths: The Mega Shredder, not counting naked clones of Oroku Saki.
- You Have Failed Me: Instead of killing Zeck and Steranko for their failure to stop the Turtles, Shredder instead sics Tiger Claw on them.
