Vilgax returns in The Flame Keepers' Circle, where he reveals that he had survived the events of his last battle with Ben. After surviving the explosion created by the fusion reactor on board his ship, Vilgax was left in a weakened state and thus unable to return to his usual form. He eventually washed up on a beach and was discovered by humans who made him into an exhibit at a traveling carnival. Although he was subjected to the indignity of becoming a spectacle for the masses, Vilgax took advantage of the situation and slowly regained his strength until a group of financialists liberated him. The Flame Keeper's Circle discovered him in his squid-like form, believing the intergalactic conqueror to be the legendary "Diagon" - an alien of wisdom and knowledge. Guided by the prophecies of their founders, the group began to worship Vilgax in the hopes that he would bring about a "Golden Age" of prosperity to the Earth through the use of alien technology. Vilgax is eventually discovered living in a fish tank in the group's main office building while Ben is out gathering information about the cult, during which he tells his arch nemesis of his plans to reclaim his empire once he gains access to a spaceship. Ben gets this information to Kevin and Gwen, who manage to disable to the Plumber's Ship that had been stolen by the cult. They attempt to expose Vilgax's true identity to the Flame Keeper's Circle, but the members remain unconvinced. Echo Echo then shatters the tank holding his nemesis, swearing to stop him if Vilgax makes another attempt to leave the Earth.
In A Knight to Remember, Vilgax is seen sulking in his aquarium, demanding that the Flame Keeper's Circle give him a means to regain his power. He learns from them that Diagon's Heart was the main source of the creature's power and quickly orders them to take him to it so that he may claim it for his own. During the ensuing battle between Diagon's cult and the Forever Knights, the weakened Vilgax stops Sir George's attempt to destroy the heart and removes the First Knight's sword from it. The power unleashed from the weapon subsequently allows the intergalactic conqueror to regain his normal form, covering him with knight armor and allowing him to absorb the heart. The Flame Keeper's Circle realizes that their leader is a fake, but Vilgax uses his newfound powers to knock out his former followers and the Forever Knights in a single blast. Winston, now possessed by Diagon, then tells Vilgax that he can gain even greater power by breaking the seal in which the Lucubra was captured. Unaware that Diagon is only using him to gain his own freedom, Vilgax travels to the site and begins to slash away at the stone with Old George's sword. Ben's team figures out the truth and arrives to stop him, but Vilgax ignores their advice. Ben then transforms into Eatle to fight him, but Vilgax proves too powerful and repels him with minimal effort, quickly using his heat vision to take down Kevin as well. He then opens the seal and gets sucked into Diagon's dimension, leaving behind the sword and armor.
In The Beginning of the End, it is revealed that while Vilgax was in Diagon's dimension, Diagon made him his most powerful follower and he became the Herald of Diagon. When Sir George arrives at the seal, Diagon sends Vilgax to fight him. The other Forever Knights attack Vilgax, but he easily defeats them, leaving George alone. After Heatblast arrives, Vilgax then moves forward towards to the seal and attempts to break it; though in remains intact, the cave wall around it crumbles and opens a void to Diagon's dimension.
In The Ultimate Enemy: Part 1, Vilgax is still battling Heatblast and Sir George. Kevin and Gwen arrive and battle Vilgax; he attacks The Seal, then Ben, Gwen, George, and Kevin. He fires at the team, however Gwen is able to shield them with a large mana field. Unfortunately, Vilgax has been able to damage the seal just enough, so that Diagon is able to produce a wave that transforms every living person on the planet into an Esoterica. Ben, Gwen, Kevin and Sir George are not effected due to Gwen's mana field, as well as Julie, whom Ship shielded from the wave by transforming into a suit around her. Every being on Earth is now under Diagon's control. Heatblast then melts the rock under Vilgax, who gets trapped and cannot escape the rock. He asks his master Diagon to give him more power, so that he may free himself and break the seal. Diagon agrees and Vilgax glows blue and grows stronger as he breaks out of the rock. He attacks Ben and George, and Ben transforms into Eatle to fight him. After a long and difficult battle, Eatle is able to ram into Vilgax and send him flying. Vilgax breaks through several buildings and crashes into the top of a pyramid.
While George and Ben think that he has been defeated, Vilgax raises up and breaks the top off of the pyramid, then throws it at them. Eatle is able to cover and protect George, but the large building falls on top of them. Vilgax crosses the wreckage and approaches the seal, then starts to destroy it. As Vilgax is attempting to destroy the seal, Diagon grows angry at him, for the power he was given was more than enough to break the seal. Eatle and George rise from the wreckage and begin to attack Vilgax. Ben mentions to Vilgax that he is not a true servant of the Diagon, and he only wants something out of it for himself. Vilgax is angered and attacks Ben again. He successfully attacks Ben and George, knocking them away. Ben transforms into Humungousaur and runs towards Vilgax. Vilgax manages to knock Humungousaur away again, and he nearly falls onto Kevin, who has arrived in the car to tell them that Diagon's got Gwen, however she snapped out of it thanks to Kevin. Gwen, George, Ben and Kevin now corner Vilgax and demand him to tell them how to stop the Diagon from coming, and how to change everyone back from being Esoterica. Vilgax asks his master Diagon for more power, but is met with silence; a ship comes in from overhead, and Psyphon exits it. Vilgax is angry that Psyphon is late, but Psyphon claims that gathering everything Vilgax asked for took more time than expected. Gwen, George, Ben and Kevin approach Vilgax and Psyphon, and Ben transforms into Jury Rigg. However, a large tremor shakes the cave, and the seal glows with a bright light, as Diagon's voice booms and reveals that it has finally escaped. The seal glows brighter, then breaks apart. Both sides approach it and look into Diagon's dimension, but find nothing. They hear his booming laugh, and run out to the cave's exposed ceiling to find Diagon in the sky, as he boasts that he is 'everywhere'.
In The Ultimate Enemy: Part 2, Vilgax and Psyphon suddenly disappear after Diagon freed himself. While Ben's team fight Diagon and his Esoterica, Vilgax waits for Psyphon to prepare the machine. After Diagon defeats Chromastone and kills Sir George, Vilgax and Psyphon return with the machine. Thinking it's a weapon, Diagon used his laser beams and tried to destroy it; however, the machine absorbs powers from other living beings and, due to Diagon's essence being only power, he was fully absorbed within the machine. Psyphon fired the machine at Vilgax, and he absorbed all of Diagon's powers. Immediately he fires his laser beams at the team, but Gwen teleports them to the Mount Rushmore Base.
Vilgax quickly finds them and sends his Esoterica to attack the base. After his Esoterica are defeated, he rips off the George Washington head and goes inside the base to fight Ben. Ben learns how to use Ascalon and the two of them start to fight. Ben stabs Vilgax and seals Diagon within the Ascalon. Defeated, Vilgax tempts Ben into using Ascalon, the Ultimatrix and Diagon's power to rule the universe. Ben begins to get tempted, but thanks to Julie, Ship, Gwen, and Kevin he snaps out of it and used Ascalon to turn every Esoterica to normal.
According to Matt Wayne, Vilgax lost the powers he stole at the end of Ultimate Alien.