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Vilgax returns in Vilgax Must Croak, where Ben and Rook had to escort him to Incarcecon, while under attack by Attea and her mercenary thugs Sixsix, Sevenseven and Eighteight who were seeking to kill Vilgax. During most of the episode, Vilgax was wearing Shock Manacles to keep him contained. While alone with Ben, he mocked Tennyson for lacking the nerve to ever finish him off, as well as the repercussions of Incursean victory. He later convinced Ben to release the shackles so they could fight Attea together, though he betrayed Ben and escaped down a shaft. He managed to avoid being caught by the bounty hunters, only to be re-shackled by Ben and forced to continue on with him. They later wound up in a stand off between their enemies and the plumbers. When Attea fired the Techadon Dissipator towards Ben, Vilgax jumped in the way, saving Ben, though he admitted he didn't know why. However, after Ben defeated Attea's group using Gravattack, Vilgax broke free of his manacles and knocked out Ben by blasting him from behind. Later, it was revealed by Grandpa Max that Vilgax went on to escape, briefly trying to take the Omnitrix, in an escape pod.
He also appears in Khyber's dream in For a Few Brains More, tied up in the back of the Rustbucket.
In Bengeance Is Mine, a human plumber by the name of Bill Gacks, (who surprisingly looks like human version of Vilgax), accidentally activates a hidden device left by Vilgax as a contingency vengeance plan against Ben. The device released an army of Squid Monsters, which Ben had fought five years prior to the Omniverse series. Following the orders of Psyphon, the monsters began a havoc in Bellwood in the name of their master, but were eventually stopped by Ben, Rook and Bill Gacks disguised as Vilgax using ID Mask.
In And Then There Were None, Vilgax has allied himself with Eon to destroy every version of Ben from every alternate reality, taking several evil Bens from the multiverse as his agents. Vilgax encountered No Watch Ben at the insistence of Eon, who believed that a Tennyson without the Omnitrix was a wildcard that they didn't need ruining their plans. Midway through the battle between multiple Bens, Vilgax activated a Chronosapien Time Bomb, a weapon that would erase all version of Ben (including Eon) and erase every alternate timeline with the exception of No Watch Ben's. This would leave only No Watch Ben, the only one that didn't stand a chance against him. While Vilgax wasted time gloating about his superiority, Professor Paradox rescued No Watch Ben from Vilgax's wrath, taking him to a pocket dimension.
In And Then There Was Ben, Vilgax is first seen when No Watch Ben and Paradox go back in time to the day where everything began. In order to reboot the prime timeline No Watch Ben disabled His ship's defenses as Grey Matter. This allowed the ship to take a last hit from Xylene's ship, making sure that Vilgax mortally injures. Back in the present, he encountered No Watch Ben a few seconds after Paradox saved him and he was glad there was one Omnitrix left. He told No Watch Ben that he doesn't even know how to use it and never will be a hero. However, he turned into Clockwork and undid the effects of the bomb. Clockwork then send back the evil Bens to their own timelines, having Vilgax left alone. Vilgax was beaten by Ben Prime, Ben 23, Gwen 10, Ben 10,000 and was given a final kick by No Watch Ben. He was then taken into custody by Alternate Max and that timeline's Plumbers.
Sometime after that, Vilgax escaped from prison and returned to the main timeline.
In Universe vs. Tennyson, he excitedly watched Ben's trial on his ship.
In Malgax Attacks, Vilgax and Albedo stole Malware's remains from the museum. They modified his genetic structure and turned him into a suit which Vilgax wore to defeat Ben Tennyson and obtain the Omnitrix. After their plan failed and Vilgax was mortally injured in the warm core's meltdown, Malware's remains start to ooze out of Vilgax's petrified body.