The group makes their last stand for New York.
- Abusive Precursors: Kraang Prime reveals that it was the Kraang who used mutagen on apes millions of years ago, creating humanity.
- Almost Dead Guy: Being dunked in freezing cold water severely drains cold-blooded Leo of what little strength he has left, but luckily he has enough fight in him left to fend off the Shredder's henchmen.
- Back-to-Back Badasses: Splinter and Leatherhead end up confronting the Shredder together.
- Be Careful What You Wish For: Donnie becomes the de facto leader of the group with Leo being out of commission.
- Big Damn Heroes: Leatherhead saves Splinter from Shredder at the construction site right as Shredder is about to kill him.
- Bloodless Carnage: Leatherhead at one point has Shredder's torso in his jaws and is heavily bashing the villain around before throwing him. No blood is visible, despite the sheer power his jaws must have as an alligator.
- Canon Immigrant: The Earth Protection Force make their debut as a rather effective organization when fighting Kraang Prime. Whether or not Agent Bishop is their leader is yet to be seen.
- Cooldown Hug: Mikey has to calm Raph down with one when it looks like Shredder has killed Splinter.
- Curb-Stomp Battle: Shredder delivers one to not just the worn-down Splinter, but to Leo and Leatherhead as well. Leo gets to deliver one to Tigerclaw, Rahzar, and Xever all at once (notably the first time Tigerclaw has been beaten by anyone other than Splinter).
- Darkest Hour: Considering that...
- Downer Ending: The Kraang have conquered New York, have begun their process of mutating the Earth, and have destroyed the lair. Kirby's been mutated again, Casey's family and the Turtles' other allies are missing. Leatherhead, Splinter, and Leo have all been beaten within an inch of their lives. The Turtles, Casey, and April are forced to run for their lives and flee New York.
- From Bad to Worse: Casey references the Technodrome incident from last year, and says that the invasion this year is actually even worse. Considering that the plot is essentially nothing but the heroes getting bested at every possible turn, this episode is built on this trope.
- Here We Go Again!: Kirby got mutated a second time.April: Not Again!
- Hippie Van: Kirby's old Party Wagon from his "hipster days."
- Internal Homage: The halfway point is a recreation of Leonardo #1 from the Mirage Comics, which was also adapted into the first movie and 2003 cartoon as The Shredder Strikes Back. While the rest of the team is at April's apartment, Leonardo (Raphael in the Movie) fights a hoard of foot soldiers in the streets, ultimately being worn down by sheer numbers. After falling in battle, his bruised body crashes through April's window, cueing the other turtles to get out of town. Defeated, they decide to take refuge at an old farm house in North Hampton to recover and plan a counter attack. Of course this version also takes place during a Kraang invasion, but it hits the major beats regardless.
- Jerkass Has a Point: Shredder remarks to his henchmen that Leo is over-confident, and judging by Leo's behavior in previous episodes, he is not wrong.
- Last Episode, New Character: The Earth Protection Force make their debut.
- Love Triangle: Averted. Donnie finally puts his feelings for April and jealousy towards Casey aside during the invasion, when previously he got distracted by it during several crises.
- Mighty Glacier: As expected for a robot that size, the Turtle Mech is pretty slow but powerful enough to take on Kraang Prime.
- Mini-Mecha: The Turtle Mech, a 3-storey sized mecha made out of spare parts that houses its pilots - the turtles minus Leo, and April - in an open cockpit setup with two in the upper half controlling each arm, one controlling the movement on the lower right and the fourth working some of the weapons on the lower left.
- Mood Whiplash: Kirby has an amusing scene where he explains that the party wagon is from his "hipster" days... and gets mutated by Kraang Prime immediately afterwards.
- Mythology Gag: With the Shellraiser destroyed, the Turtles take Kirby's old "party wagon" as their new mode of transport.
- Mikey's line "Turtle Mech power!"
- No-Holds-Barred Beatdown: Tigerclaw, Xever, and Bradford deliver a brutal one to Leo, however brief it is.
- Nothing Is the Same Anymore: You bet.
- The Reveal: Kraang Prime reveals that the Kraang essentially created humanity by using mutagen on monkeys.
- Sequel Hook: Karai saves Splinter from drowning.
- Shock and Awe: The Turtle Mech's final attack has it redirecting the electricity from a power line and firing it at Kraang Prime.
- Tragic Monster: Kirby is mutated again, this time into a Kraang version of a human.
- The Voiceless: Xever never speaks during the two parter unlike Bradford and Tiger Claw.
- What Happened to the Mouse?: Leatherhead, Casey's family, Murakami, Kurtzman, and all of the other mutants' fates are unknown.
- You Can't Go Home Again: It finally hits home in this part of the finale, as the Turtles retrieve what little they can from their destroyed lair.
- You Monster!: After seeing Shredder seemingly kill Splinter and throw him into a storm drain, a raging Raphael yells this at him.
