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 1 and the bounty hunter Armaggon.
At one point during their adventures throughout the cosmos, April is given a fragment of the ancient Aeon's mystical Sol Star (containing the very essence of power and life itself), and which helps her in further developing her psychic abilities as well as drastically increasing them to incalculable levels; also due to the several training sessions she had with the Fugitoid.
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 it is revealed Karai is back, She was her friend before brain worm was vanished and intends to rebuild the Foot Clan and dispose of Shredder who is still recuperating from his last fight with Splinter.
Furthermore, some other crime organizations have been plotting to take over the Foot Clan's territory, and a crystal fragment of immeasurable mystical power (which April had received from an ancient benevolent race of aliens known as the Aeons) is beginning to exert quite a baneful influence on her.
She then apologizes to her friends for not disregarding the universal influence the Sol Star fragment had on her, but assures everyone that she now has a better understand of how to control her increasingly powerful psionic abilities on her own.
It is revealed that Shredder is alive but gravely injured from the previous episode who now uses mutagen provided by Stockman to speed up his recovery and to further increase his strength.
As Super Shredder prepares for the final blow, Splinter throws a knife at some smoke bombs, which causes the ledge to crumble and collapse, resulting in the longtime rivals to fall 1,000 feet into the abyss below; presumably to their deaths.
Fortunately, April uses her extraordinarily powerful telekinetic abilities against Super Shredder and succeeds in saving Karai from being crushed by a truck that contains sulfuric acid (thanks to the mystical Sol Star fragment further amplifying her psionic abilities), her eyes glow a bright blue and she smiles malevolently as she hurls it right back at Super Shredder.
Tokka, who is shown to have survived the colossal implosion of the dwarf star in "The Ever-Burning Fire", returns and discovers that her baby boy (whom Raphael adopted as Chompy Picasso) is missing.
A dangerous female assassin and fox-mutant, by the name of Alopex, with super speed, appears who is bent on taking down her own brother, Tiger Claw, with the cursed Blades of Vengeance.
Tiger Claw shoots her from behind, but Alopex anticipates this and dodges the blast and slices off his right arm; an act that shocks even the Turtles.