After the Turtles, April, and Casey are saved from the destruction of Earth, the Fugitoid uses his spacecraft the Ulixes to turn back time to six months earlier in order for him and the Turtles to prevent the Triceraton Empire led by Emperor Zanmoran from assembling the three components of the Heart of Darkness that are scattered throughout the universe before everything on Earth is lost. Besides fighting the Triceratons, the Turtles also face new enemies in outer space like Lord Vringath Dregg of the planet Sectoid and the bounty hunter Armaggon, and even have an adventure with their interdimensional 1987 counterparts and their enemy Krang who is an exiled relative of Kraang Subprime. Despite the efforts of the Turtles, the Triceratons are still able to collect all three pieces of the Black Hole Generator, only for the Turtles to return to Earth and join forces with their past selves to warn Splinter before he is killed by the Shredder, stop the detonator of the Heart of Darkness, and defeat the Triceratons. The Fugitoid destroys the Black Hole Generator near the Triceraton spacefleet, causing to explode, presumably killing the Triceratons. In the aftermath of the fight against the Triceratons, the past versions of the Turtles, April, and Casey leave Earth with the past Fugitoid in the Ulixes while the present Fugitoid’s head reactivates in Earth orbit.
Weeks later following the Triceraton Invasion being thwarted and the Foot Clan’s disappearance, April is promoted to kunoichi at the time when the witch Shinigami arrives and is revealed that she is Karai’s friend as they plot to rebuild the Hamato Clan and dispose of Shredder who is still recuperating from his last fight with Splinter. While Karai and Shinigami got some ninjas on their side, the Foot Clan strengthens the Footbot army by creating the Elite Footbots. Furthermore, some other crime organizations have been plotting to take over the Foot Clan’s territory, and a crystal shard of unimaginable power which April received from the alien Eons during their space adventure is beginning to exert a baleful influence on her. Using a special mutagen formula, Oroku Saki recuperates and becomes Super-Shredder in order to take back control of the Foot Clan.