In this third and final installment, the Turtles have become celebrities around the city of New York, but their partying with celebrities and fans gets them to lose their purpose of defending the city, and suddenly the city becomes mutated as they have to save the world again for one last time.
- Ninja Turtles: having become heroes of New York, they forget their duties of saving the world when hanging out with celebrities and fans, and partying
- Leonardo (Pete Ploszek)
- Raphael (Alan Ritchton)
- Michelangelo (Noel Fisher)
- Donatello (Jeremy Howard)
- Master Splinter (Tony Shalhoub) - becomes disappointed with the Turtles’ misbehavior and partying, and tries to get them to learn their duties, he fights Kraang and gets hurt, then realizes the mutations that made him blend in.
- April O’Neil (Megan Fox) - having got her job as Newscaster under her new boss, Rita, she does a relationship with Casey, during the mutation, she becomes a humanoid lion, as Cat April
- Casey Jones (Stephen Amell) - began a relationship with April and rents an apartment with her
- Irma Sinclair (Ashley Johnson) - April's old friend from High School, and is Donatello's love interest.
- Vern Fernwick (Will Arnett) - now the Editor of Fernwick Studios, he helps the Turtles deal with Agent Bishop.
- Leatherhead (Michael Leon Wooley through motion capture) - a mutant Saltwater Crocodile who became friends with the turtles, and helps them with tough missions.
- Professor Honeycutt (Martin Freeman through motion capture) - April's old tutor who entered an alien robot body.
- Mona Lisa (Gabriel Union through motion capture) - Raphael’s love interest, She was the lost experiment from the explosion in TGRI.
- Rita Braggart (Judith Hoag) - April’s new boss, who develops a friendship with her, as she and April are “like the same person”
- Agent Bishop (Luke Evans) - serves as the head of Earth Protection Force, who is the Turtles’ ally at first, helping them with an invading force called, the Triceratons, and to prepare themselves with Kraang, only to turn out around the Mutation act, he comes out as the film’s true main antagonist, whose goal is to TGRI the ultimate Cure, as he is the one who took advantage of Raphael's accident with destroying the vile and expanded it in the sewers.
- Foot Clan: share the role of the quaternary antagonists with Bebop, Rocksteady, Tokka and Razhar, they became a TGRI unit.
- Shredder (Brian Tee) - returns as the film’s secondary antagonist, works with Bishop witht he scheme to take revenge on the Turtles and Kraang.
- Karai (Brittany Ishibashi) - she gains conflicting loyalties to her master when she doubts her family heritage as Shredder’s daughter, as she becomes tangled with Leo in a “dating Catwoman” relationship, She was killed by Bishop.
- Bebop and Rocksteady (Gary Anthony Williams and Sheamus) - share the role of the quaternary antagonists with Tokka, Razhar and the Foot Clan, they have an old friendship with Tokka and Razhar, they were beaten by Donatello and Michelangelo.
- Tokka and Razhar (Daniel Wu and Steven Blum) - share the role of the quaternary antagonists with Bebop, Rocksteady and the Foot Clan, they started out as arms dealers then became a Snapping Turtle and Dingo, they were defeated by Leonardo and Raphael.
- Kraang (Brad Garrett) - returns as the film’s tertiary antagonist, he gets captured after Splinter defeats him.
- Triceratons: the film’s quinary antagonists, aliens that came for the Omnidroid.
- General Braxis (Adam Baldwin through motion capture) - head general of the Triceratons.
- Lieutenant Darcy (Michael B. Jorden through motion capture) - the only Triceraton with honor that reveals Bishop's motives.
- Celebrity cameos:
- Albert Brooks - shows as the person April interviews on the Triceraton crisis.
- Donald Sutherland - shows as a blind man playing chess with Splinter.
- Bruce Greenwood - acts as a police officer who called Agent Bishop for the Turtles.
- Nicki Manaj - acts as a girl who has a crush on Michaelangelo and kisses him.
It begins in space when the Triceratons captured Kraang, and demanded that he surrendered the Omnidroid, instead he gave them Shredder who is thawed and wants revenge for his betrayal. The Triceratons agreed but needed him alive, Kraang then gave up the Turtles in exchange for his freedom.
On Earth in New York the turtles are partying in Fernwick's Studios acting as mascots for Vern, when Splinter saw the news he was disappointed but had a thought before he left about his past. The Turtles partied and Casey and April try to tone it down. Michaelangelo then is dancing with Nicki and slaps her butt, she then states "I'm not the only one!", pointing at April. Splinter arrives and was going to berate them but sees why they are partying with Celebrities when Tokka and Razhar are in play. This reveals to Splinter what the party was all about to bait the Foot Clan in.
After the fight in the party, Splinter reminds them of their role as ninja, then reveals to April the whole truth, revealing if she remembered Hamata Yoshi, which she remembered, he revealed that Hamata Yoshi died and left the rat with her father years ago. Leonardo accepts the responsiblity, but Splinter states "It's not just your fault you did it to bait out the Clan, but your brothers are also the blame, they are old enough to own up to their mistakes as well!". Meaning anyone can be a leader to their own destiny.
They are introduced to Agent Bishop in the next day with a group of CIA agents he reveals that the Shredder is alive and is allied with the Triceraton. Splinter was shocked to hear this and agrees to this proposal, meanwhile Irma, April's old High school pal came to visit her when Casey was gonna propose. April accepts the proposal and makes Irma the maid of honor, She then meets the turtles which gave her a fright until Donatello calmed her down. Agent Bishop then was seen talking to Leonardo and Splinter about the canister which came back to haunt Raphael.
They reach the headquarters of the Triceraton on a shuttle and fight off the Triceraton forces that came out of nowhere when they entered the ship. But Donatello stayed behind to help Irma get use to the turtles, he then notices a smoke coming out from the toilet and covers Irma's mouth. April comes in an smells it, Casey witnessed as she turns into a humanoid lioness she was shocked at her reflection and tries to let Donatello know that it's not their fault, both Casey and April are lions and walks out seeing the whole city mutated into animals.
The other three and Splinter confront Kraang and the Triceratons, Agent Bishop then runs and grabs the Omnidroid hidden in a bunker in Kraang's ship, revealing Kraang was lying about the turtles having it. Kraang was defeated by Splinter who was wounded in the process, one Triceraton warns Raphael not to trust Bishop, and reveals Operation TGRI, revealing that Bishop is a member of the Foot Clan, and the adopted son of Shredder. Bishop kills the Triceraton heads revealing the truth. April spied on the probe on the Omnidroid that Irma gave her revealing he orchastrated Tokka and Razhar who were then mutated in prison, they reunite with Rocksteady and Bebop.
As the Turtles and Splinter are in a cell by Bishop, they see the city mutated into a Safari Zone, they even see Vern as a humanoid Hawk. Bishop reveals that he too is mutated by the same mutation and tells them that Kraang, and what happen to them years ago were planned from the beginning, he sees as mutant animals makes them more evolved that normal. After Bishop leaves a Crocodile named Leatherhead reveals that he was once a man named Proctor then was mutated with Rocksteady and Bebop revealing he was there and was the janitor, The Omnidroid reveals himself as Prof. Emmett Honeycutt and is the way he is because of Bishop.
Back on earth April tries to contact her new boss whom she made friends with, only to realize she was working for Bishop and was mutated into a snake, which Vern apprehends her and she confesses that her old boss knew all along and wanted to see if she was as arrogant enough to turn a story into an obsession. Causing April to realize that Channel 6 was on their payroll, Casey comforted her and Donatello remembered it can make them human again, but remembered that Raph destroyed it. Back on the Ship Raph regret it destroying it. Splinter then apologizes for being harsh with them and not realizing that if they give others a chance then they would given a chance to be considered among them. Honeycutt cuts the bolts off the doors and frees them.
Bishop witness April and Casey on a screen helping the people and informs the Shredder what he must do. Shredder then has him bring Rocksteady, Bebop, Tokka and Razhar on the ship to ready the army. Raphael gets seperated by door and tells the others he will find them, he meets Mona Lisa and helps her escape the torture chamber where he battles Razhar, meanwhile Splinter and Leatherhead battle Kraang, as Michaelangelo reaches the control pannal and has to get pass Bebop in the process, Tokka and Karai ambush Leonardo and almost kills him, but April came out from the portal made by Honeycutt to battle Karai as Leo battles Tokka.
Donatello and Irma meet Prof. Honeycutt who confronts Rocksteady who guards the power core. Casey enters the heart of the ship and confront the Shredder. The Turtles defeats Rocksteady, Tokka, Bebop, and Razhar but Karai and April are still battling. Bishop is seen in the naviagation room and stabs Prof. Honeycutt, Irma recognizes him as "Jarred Queen" an old student of Honeycutt revealing he wanted revenge for his humiliation by humanity years ago. April was knocked out by Karai and battles Leonardo she then realizes that she is Hamata's lost daughter, and then has regrets. She is killed by Bishop for failure, enraging the Shredder who realized it was Bishop's jealousy of Karai that kept him in line.
Leo now enraged battles Bishop who mutates into a demonic Wolf, which Raph, Donnie, and Mick joins in to battle the mutated Bishop. Shredder was going to blow everyone up in the ship but was stabbed by Casy with a Katana he used to kill Hamata Yoshi. Leonardo and the brothers come up with a plan, while Mona takes April and the others out. They fight him and remembered Splinters words that it's everyone's responsibility. They all defeat Bishop and launches him inside the core and exploding with him in it. The Four defeated Animals led by Kraang escapes inside a pod and ends up in custody of the real CIA agents.
Leo and the brothers enter a pod and landed inside the Atlantic Ocean. Back in the city everyone mutated were treated by Donnie and Irma's cure except April, Mona, and Leatherhead they sacrificed the cure so the people needed it more. The Turtles arrive on a Raft made from Kraang's ship and were seen as true heroes, even Splinter was proud to see that they accepted responsiblities.
- Teenage Mutant Ninja Turtles (2012 theme song) - played during the beginning.
- It Takes Two - by Rob Base and DJ EZ Rock, played during the battle between Karai and Leo.
- Party Up - by DMX, played during the party the turtles participated.
- Party Rock - by LMFAO, played during the fight with the Foot Clan.
- Radioactive - by Imagine Dragons, played during when Mutation begins in New York.
- Pump It - by Black Eyed Peas, played during escape from Rocksteady, Bebop, Toka, and Razhar.
- The Triceratons were advertised as the main antagonists, but it turns out Agent Bishop is the true main antagonist.
- The film is rated PG for violence, and scary images.