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- S2.E1 ∙ The Mutation Situation
- S2.E2 ∙ Invasion of the Squirrelanoids
- S2.E3 ∙ Follow the Leader
- S2.E4 ∙ Mutagen Man Unleashed
- S2.E5 ∙ Mikey Gets Shellacne
- S2.E6 ∙ Target: April O'Neil
- S2.E7 ∙ Slash and Destroy
- S2.E8 ∙ The Good, the Bad and Casey Jones
- S2.E9 ∙ The Kraang Conspiracy
- S2.E10 ∙ Fungus Humungous
- S2.E11 ∙ Metalhead Rewired
- S2.E12 ∙ Of Rats and Men
- S2.E13 ∙ The Manhattan Project: Part 1
- S2.E14 ∙ The Manhattan Project: Part 2
- S2.E15 ∙ Mazes & Mutants
- S2.E16 ∙ The Lonely Mutation of Baxter Stockman
- S2.E17 ∙ Newtralized!
- S2.E18 ∙ Pizza Face
- S2.E19 ∙ The Wrath of Tiger Claw
- S2.E20 ∙ The Legend of the Kuro Kabuto
- S2.E21 ∙ Plan 10
- S2.E22 ∙ Vengeance is Mine
- S2.E23 ∙ A Chinatown Ghost Story
- S2.E24 ∙ Into Dimension X!
- S2.E25 ∙ The Invasion: Part 1
- S2.E26 ∙ The Invasion: Part 2