The season begins with the Turtles, April O'Neil and Casey Jones retreating to North Hampton, after being separated from Splinter.
They later return to New York City, and join forces with the Mighty Mutanimals to fight off the Kraang, and prevent them from taking over Earth.
The Turtles later end up travelling in time, back England in the Middle Ages, and to Japan 16 years earlier, witnessing the conflict between Hamato Yoshi and Oroku Saki.
The season ends with the Triceratons being spotted on Earth, and the conflict between the Kraang and the Triceratons leading to the destruction of Earth when the Triceratons use the Heart of Darkness, right after Shredder has killed Splinter.
Right before Earth is destroyed, the Turtles, April O'Neil and Casey Jones are picked up by Zayton Honeycutt in his spacecraft Ulixes. They fly away into outer space, and travel back in time to prevent the Triceratons from destroying Earth.
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