In the Time Nest, headquarters of the Time Patrol, the Supreme Kai of Time informs Xeno Trunks and Xeno Pan that her mystical bird Toki-Toki has disappeared. She sends the two of them to find him, while also being worried about a supposed "Bird of Catastrophe" that has been released. Meanwhile, Toki-Toki has appeared on Earth in the main timeline, where Goku finds him while training with Vegeta, Gohan, Piccolo, Krillin, and Android 17. Xeno Trunks and Xeno Pan arrive and are happy to see that Toki-Toki is safe, with Xeno Pan explaining that his existence is very important for the inner workings of the multiverse. Suddenly, the group is interrupted by the arrival of all twelve Gods of Destruction.

Goku, Vegeta and Xeno Trunks are fighting against Beerus, while the others and the other Gods of Destruction watch. Beerus has the upper hand, until their battle is interrupted by the arrival of Xeno Goku and Vegeta, who warn them that they need to stop the fight. Suddenly, a mass of giant tree roots appears in the sky around the Earth and begins draining the planet's energy. The other gods all rush back to their own universes to protect them, leaving Beerus, the Earth's heroes, and the Time Patrollers behind. They are then confronted by Fu, who is accompanied by Doki-Doki. Fu confirms that this is the "Bird of Catastrophe" that Beerus was worried about and that the tree roots are part of the Universe Tree, which grew from the Universe Seed that Hearts was developing. Fu escapes through a portal. Beerus rises into the sky and powers up, shielding the Earth by allowing the Tree to feed on his energy instead; however, he warns the others that he will not be able to keep this up for long.

Fu, accompanied by an unknown female companion, meets with a group of villains - Meta Cooler, Turles, Bojack, Super Android 17, and a mysterious humanoid scientist known as Dr. W - on the Universe Tree, where he reveals that he rescued all the villains from the moments before their deaths at the hands of the Z-Fighters and convinces them to help him in exchange for places in the new universe that he is creating. Meanwhile, Goku, Vegeta, Xeno Trunks and Xeno Pan are searching for Fu, when they are attacked by Turles and Bojack. The two villains reveal that Fu has been able to increase their power immensely, as they are now strong enough to fight on par with Goku and Vegeta's Super Saiyan Blue forms and have auras similar to Cumber's. As the battle rages, Xeno Trunks spots Fu observing the fight: Goku and Vegeta try to engage him instead, but Turles and Bojack block their way. Elsewhere, Xeno Goku and Xeno Vegeta arrive in Hell, and are confronted by the mysterious Dr. W.

Dr. W begins what he calls an "analysis" of Xeno Goku and Xeno Vegeta by attacking them with strange, teleporting energy blasts. They both power up to Super Saiyan 3 and engage him in combat, but he is able to hold them both off with his strange attacks and high-speed reflexes. After having difficulty overpowering him, they power up to Super Saiyan 4 and land a powerful combined blast on him; however, Dr. W deliberately takes their attacks head-on, and emerges from the smoke with a glowing golden aura identical to theirs. Having completed his analysis, he then opens a portal and escapes. Meanwhile, Fu is observing the battle between Goku, Vegeta, Turles and Bojack. He releases Doki-Doki, who generates waves of dark energy that immobilize Goku, Vegeta, Xeno Trunks and Xeno Pan. Toki-Toki tries to defuse the dark energy, but Fu traps him and throws him through a portal, before recalling Doki-Doki and escaping through one himself.

In Hell, Xeno Goku & Xeno Vegeta, even both as super saiyan 4, struggle against the reborn Janemba, who is aware of all of their abilities and tactics, which enable him to easily overwhelm both saiyans. Just when Janemba is about to finish them off, Xeno Trunks, Xeno Pan, Goku & Vegeta arrive in Hell through a wormhole, joining in on the fight. Xeno Trunks powers up to Super Saiyan 3, while Goku & Vegeta both power up to Super Saiyan Blue. Super Saiyan Blue Goku And Super Saiyan 4 Xeno Goku then team up and begin to overpower Janemba with their simultaneous attacks. But not long after, Putine & Majin Salsa arrive in Hell and knock back Janemba, enraging Dr. W by interfering in the fight.

Xeno Trunks identifies the new arrivals, Majin Salsa and Putine, as demons and old enemies of the Time Patrol. However, the demons offer to help the heroes in their efforts to destroy Fu's Universe Tree, warning that the Tree is continuing its work of consuming countless planets across the multiverse. Janemba attacks them all again before the two groups can come to an agreement, and the battle resumes, with Xeno Trunks powering up to Super Saiyan God. Majin Salsa suggests that Xeno Goku and Xeno Vegeta use a mysterious technique that they have employed in the past, so the other Saiyans all power up and channel their energy into the pair while the two demons hold off Janemba. By absorbing the others' energy, Xeno Goku and Xeno Vegeta break through their limits and achieve a higher level of strength, known as Full-Power Super Saiyan 4. They attack Janemba together, succeed in overpowering him, and are finally able to destroy him using their ultimate technique, the Double Dragon Fist.

Goku, Vegeta, Xeno Goku, Xeno Vegeta, Xeno Trunks, Xeno Pan, Majin Salsa and Putine arrive on the Universe Tree, which is still absorbing energy from the multiverse. Vegeta attempts to destroy the Tree with a large ki blast, but it absorbs the energy instead. Fu then appears and confronts the group, informing them that he plans to create a new universe using the Tree. Xeno Goku, Xeno Vegeta, Xeno Trunks and Xeno Pan are suddenly teleported away by Fu's female companion, who is revealed to be Towa; she tells Fu that she is doing something for him, and then teleports away along with Majin Salsa and Putine. Vegeta powers up to Super Saiyan Blue and attacks Fu, but Fu reveals that he now has access to Cumber's energy and channels Cumber's aura through his own body, using its effects to corrupt Vegeta's ki and drive him berserk. Goku tries to intervene, but Fu corrupts his ki as well.

Fu is horrified by the Universe Tree's death, until Towa and Mira arrive to help him. Towa infuses Mechikabura's energy into Fu, dramatically increasing his power and causing him to undergo a transformation into the new Demon King. However, Fu expresses no interest in this, and begins using his new powers to restore the Tree instead. Vegito tries to stop him and their fight resumes, but Towa and Mira intervene to help Fu and buy time for him by attacking Vegito. Before Fu can finish restoring the Tree, however, a portal opens and Xeno Vegito emerges, now powered up to Full-Power Super Saiyan 4 and accompanied by the Demon God Demigra. Xeno Vegito attacks Fu, and the battle resumes. Meanwhile, in an unknown location, an alternate version of Broly awakens.

Xeno Vegito begins fighting Fu; the two of them seem to be evenly matched, until Fu uses his dark magic to change the area around them. He manifests a large combat arena for them to fight in, and prepares to engage both Vegitos in battle until the three of them are interrupted by the sudden arrival of the alternate Broly in his Legendary Super Saiyan form. Xeno Vegito overpowers Broly, until Broly also transforms into a Full-Power SS 4. The main timeline's Vegito joins the fight and the two Vegitos battle Broly together, but even the two of them together struggle against his monstrous power. Meanwhile, Fu uses his magic to fully revive the Universe Tree. The main-timeline Vegito continues fighting Broly, while Xeno Vegito goes after Fu, but the Tree suddenly releases a massive wave of light that engulfs Fu, Broly, and the main-timeline Vegito. Xeno Vegito escapes, while Majin Salsa, Putine, Dr. W, Turles, the captive Cumber and Hearts's spirit body are all enveloped by the energy wave.

Xeno Vegito outruns the energy wave before it dissipates, leaving the area around the Tree unscathed; he returns to find Fu holding the miniaturized form of the new universe created by the Tree. However, Fu is disappointed by his creation, as the new universe is flawed because Fu had to use his own demonic power to refuel the Tree rather than the pure energy of a normal universe. A furious Xeno Vegito attacks Fu, determined to stop him from doing anything else, and their battle resumes. Towa challenges Demigra, but his female companion takes her on instead, while Demigra uses a mystical technique known as "Time Labyrinth" to freeze both Xeno Vegito and Fu in time. Towa claims that Fu will be able to escape the frozen-time bubble, but Demigra is confident that he will not. On Beerus's planet in the Seventh Universe, Whis and Vados sense the creation of the flawed new universe. Meanwhile, in the new universe, Goku awakens alone, in a strange, empty version of West City.