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- Season 2 overviewOct 12, 2013-Sep 26, 201426 episodesSeason 2 episodes1. The Mutation Situation Oct 12, 2013
- The turtles' problems worsen when Shredder teams up with the Kraang to receive a batch of mutagen.
- 2. Invasion of the Squirrelanoids Oct 19, 2013
- The Turtles bring a mutated squirrel back to the lair.
- 3. Follow the Leader Nov 2, 2013
- Karai captures Leonardo and forces him to do battle with ninjas that can adapt to his every move.
- 4. Mutagen Man Unleashed Nov 9, 2013
- Donatello experiments with mutagen in an attempt to find a cure for April's mutated father.
- 5. Mikey Gets Shellacne Nov 16, 2013
- Michaelangelo plays with some mutagen, contracting a dangerous infection.
- 6. Target: April O'Neil Nov 23, 2013
- April realizes that she may have put her friend in jeopardy when Karai starts hunting her again.
- 7. Slash and Destroy Nov 30, 2013
- The Turtles are hunted by a mutant turtle named Slash, who has a personal vendetta.
- 8. The Good, the Bad and Casey Jones Feb 2, 2014
- Casey Jones and Raphael must put their dislike for each other aside and work together.
- 9. The Kraang Conspiracy Feb 9, 2014
- April feels left out and insists on joining the Turtles on a mission to TCRI.
- 10. Fungus Humungous Feb 16, 2014
- A fungus mutant spreads through the sewers causing the Turtles to experience their worst fears.
- 11. Metalhead Rewired Feb 23, 2014
- After Donnie upgrades Metalhead's artificial intelligence, he must decide if he can trust him.
- 12. Of Rats and Men Mar 2, 2014
- When the Rat King returns, Splinter must overcome his fears in order to defeat his enemy.
- 13. Wormquake! Mar 14, 2014
- Leonardo considers asking Splinter for help while facing Shredder's new assassin.
- 14. The Manhattan Project Mar 14, 2014
- Leonardo considers asking Splinter for help while facing Shredder's new assassin.
- 15. Mazes & Mutants Apr 27, 2014
- The Turtles try to relax by playing a role-playing game, but the game becomes real.
- The Turtles create a retro-mutagen to help April's father; Baxter Stockman threatens April.
- 17. Newtralized! May 11, 2014
- Raphael is worried about Casey's ability to handle big mutant threats; Slash has a new partner.
- 18. Pizza Face May 18, 2014
- Mikey struggles to convince the others that a new mutant is trying to attack and capture people.
- 19. The Wrath of Tiger Claw Jun 8, 2014
- When Tiger Claw returns, he vows to destroy the Turtles.
- 20. The Legend of the Kuro Kabuto Jun 15, 2014
- Leo tries to convince the team to rescue Karai; a master thief steals Shredder's helmet.
- 21. Plan 10 Jun 22, 2014
- Raphael accidentally damages a machine that forces him to swap minds with a Kraang.
- 22. Vengeance Is Mine Jun 29, 2014
- Leo stages a rescue for Karai against Splinter's wishes.
- 23. A Chinatown Ghost Story Sep 12, 2014
- Donnie becomes increasingly jealous of April and Casey's relationship; April is kidnapped.
- 24. Into Dimension X! Sep 19, 2014
- Mikey is the only one who can figure out the bizarre realm of Dimension X.
- 25. The Invasion Sep 26, 2014
- Leo and Donnie disagree about their plan to stop the Kraang invasion; Donnie steps up as a leader.
- 26. The Invasion Sep 26, 2014
- Leo and Donnie disagree about their plan to stop the Kraang invasion; Donnie steps up as a leader.