Plot
In the dimension of Teen Titans Go!, the Teen Titans were installing their new television, when Beast Boy finds a strange crystal on the floor, and places it on the shelf using it as a bookend, when then Control Freak arrives, who announces to the Teen Titans that they will have a new superhero crossover. So they all decide to watch the movie.
Elsewhere in the Multiverse, on the dimension of DC Super Hero Girls, the Super Hero Girls fight against their enemies Super Villain Girls, that manage to escape through a portal that opened behind them. The girls investigate and discover that the chain of events is related to Cythonna, the Kryptonian Goddess of Darkness, Plague and Suffering, who many years ago her brother Rao locked her in an Amulet and banished to space.
However, the Amulet had been found by Lex Luthor, which he used to rescue the villains of Metropolis and form the Legion of Doom, planning to get rid of the superheroes by locking them in the Phantom Zone. The now formed team wreaks havoc through Metropolis to lure the heroes out and lock them up. The team of heroines gathers in the park, and they find a strange rune with Cythonna's name inscribed on it. Being a clue of Kryptonian origin, Supergirl goes to her cousin Clark to translate it. But Clark ignores her believing that Cythonna is just a legend, but he warns the Justice League that she knows about the Phantom Zone.
The girls head to the Fortress of Solitude to search for information about Cythonna and her Amulet. But they are confronted by the Superman Robots, and then the real Superman and the Justice League. The girls refuse to give in, and fight the League, until Wonder Woman stops the fight and hands the crystals to Superman, deciding to leave the rescue plan in the hands of the League, much to the girls' displeasure. Batgirl however had secretly stolen the crystals, with the information they needed. Meanwhile, Wonder Woman receives a secret call from Batman, asking her to meet at the Daily Planet, where he and Superman tell her to join them to stop Luthor and the Legion.
Back at the base, Supergirl and her friends are watching a message from her uncle Jor-El, who gave his son a message about the Amulet of Cythonna; and the girls discover that it contains the essence of the Goddess of Darkness and plans to free herself from her prison by feeding on the souls of the wicked, use a Kryptonian vessel and claim the universe as her domain. Assuming that it is Cythonna controlling Luthor and not the other way around, the girls come to the conclusion that the League underestimated the real enemy they face, and try to call Wonder Woman to warn her, but she doesn't answer.
Lex Luthor continues to prepare his plan to claim dominion of the world, but Cythonna controls him. As the crystal of the Amulet slowly shatter, she grows stronger. The League heads to the Legion of Doom's base, preparing an assault to rescue the trapped heroes. The League confronts the Legion members, but they turned out to be holograms.
Superman is locked in a Kryptonite box and the rest of the League is trapped in the Phantom Zone, leaving only Wonder Woman. Surprisingly, Harley Quinn secretly helps her escape the Hall of Doom. The girls dispute over the choices Wonder Woman made and dissolve the team. Out of guilt, Wonder Woman returns to her old home Themyscira.
Lex announces to the world that they will take over the world. Hearing Luthor's announcement, Bumblebee sends an emergency call to her friends to meet at the junkyard, where she encourages them to team up again to save the world and defeat the Legion of Doom. For her part, Harleen (who quit the Legion and reunited with Batgirl) retires and leaves the girls behind, claiming that she isn't interested in saving the world.
The girls go to Themyscira, reconcile with Wonder Woman, and they all return to Metropolis. Having no other choice, the United Nations gives the world to the Legion of Doom, and all the villains celebrate their victory. Cythonna, who plans to use Supergirl as her new host, uses Superman as bait to lure her out and succeeds in trapping her. The rest of the Super Hero Girls try to get to the Phantom Zone with the help of Zatanna’s dark magic, which accidentally strands them in the TTG dimension, where they meet the Teen Titans.
While in the TTG universe, the Teen Titans help the Super Hero Girls with fixing Bumblebee's computer and giving the resources they need to return to their universe, and Zatanna receives words of encouragement from Raven that help her accept her dark entity. Zatanna transports herself and the team, and they return to their universe heading towards the Phantom Zone.
The Super Hero Girls arrive at the Phantom Zone and rescue their friends, as Cythonna breaks free of the shattered amulet. The Legion of Doom battle the Super Hero Girls, the Invinci-Bros, and the Justice League, but are defeated. Supergirl pretends to surrender to Cythonna and allows her to possess her, but she is overpowered by the girls. Supergirl pulls out a crystal and imprisons Cythonna inside it, freeing herself and, along with Zatanna, banish Cythonna out of her universe. The girls, along with reformed Harley Quinn celebrate at Sweet Justice.
The Teen Titans are disappointed not to have been on their adventure with the girls, even though Control Freak had told them that they play an important role at the end of the story, but to their surprise, Cythonna had possessed Control Freak to retrieve the crystal again. Teen Titans foil her attempt to destroy their universe, and she is once again fully defeated and banished by Raven, ending up stranded in the dimension of Super Friends. The Super Friends plan to send the crystal back, but they take one look at the Teen Titans fighting over the remote and decide not to.
