At some point, Vilgax is fending off the Highbreed's invasions on his territories.
Vilgax returns in Vengeance of Vilgax, having come back in a currently unknown way. His appearance has changed again; he is less cybernetically enhanced and his mouth is visible again. In addition to his traditional army of drones, he has been joined by new alien assistant, Psyphon. In order to justify his invasions, he now follows a Galactic law, fighting champions of a planet he attacks and defeating them to gain the right to legally conquer that world. In this manner, he conquered ten worlds, the last of which was Ultimos', and absorbed the champions' powers with the help of Psyphon, giving him powerful, new abilities. Despite all of his new-found power, Vilgax retains his obsession with the Omnitrix.
After his victory against Ultimos, Vilgax returns to Earth, where he quickly defeats Max and the Plumbers' kids. He does not however, choose to absorb their powers and instead uses them as messengers to Ben, challenging him in the rules of the Galactic Code, as he did with his other conquered planets, and leaving him 24 hours to answer, after which Vilgax will enforce his legal right to destroy Earth. After accidentally overloading the Omnitrix which mutates Kevin and recollects his escaped aliens, Ben comes and fights him. After a long and feral battle, Vilgax eventually smashes Chromastone to pieces, seemingly killing him. However, as Vilgax is about to take the Omnitrix, it reformats Chromastone's remnants into Diamondhead, bringing Ben back to life. Due to both his age and the practice he had with this form during summers, Diamondhead proves to be strong enough to defeat Vilgax, and the Galactic Conqueror, according to the laws, is forced to leave Earth with his army and never come back. He begrudgingly accepts his defeat, but vows to get revenge on Ben one way or another.
Although Vilgax is manipulating the rules of the Galactic Code (which were established by the Galvans to prevent the massive loss of live) for an evil purpose, he does follow through on his adherence to them, despite his plan back firing.
In Ghost Town, Vilgax breaks Zs'Skayr out of his prison in exchange for the secrets of the Omnitrix. However, Zs'Skayr betrays him and invades his homeworld, Vilgaxia, by possessing the majority of its inhabitants and turning them in Ectonurite slaves. After vainly fighting the invasion, Vilgax escapes and reluctantly asks help from Ben and his team. After an uneasy alliance between them, they eventually reached Zs'Skayr, and Ben let himself be possessed in order to absorb him back into the Omnitrix. Though it was successful, Zs'Skayr took over Ben's personality, resulting in a battle between Ben's team, Vilgax, and himself (the former two parties now in contention over whether or not Zs'Skayr should be harmed while in Ben's body). Vilgax was eventually able to produce enough light to weaken Zs'Skayr, allowing Ben to take over again and turn back to human form. Vilgax then allows Ben, Gwen, and Kevin to leave, having earned their freedom for their help. Vilgax later gloats to himself about having acquired the secrets of the Omnitrix.
In Primus, Vilgax attacks the planet, Primus, causing the Omnitrix to teleport Ben, Gwen and Kevin to the world as well. The Omnitrix leaves Ben's wrist to find Azmuth. Azmuth uses the Omnitrix himself to fight Vilgax and protect Primus. Vilgax defeats Azmuth and takes the Omnitrix from him. As the device has recalibrated since he last operated it, Vilgax no longer knows how to use it, forcing him to ask Ben for the information in exchange for his friends' lives (after taking them captive).
Ben activates the Omnitrix, turning Vilgax into Goop, but Ben steals the artificial gravity disk and turns it off; leaving Vilgax as an immobile puddle. Ben takes the Omnitrix out of the puddle of Vilgax as Goop, changing Vilgax back to normal and then re-attaches the device to himself. Cannonbolt throws Vilgax into the Codon stream (which is full of the DNA the Omnitrix accesses to transform its wearer) where he grows considerably larger. Ironically, at the end of this episode Ben throws Vilgax into space after changing into Way Big similar to Vilgax's defeat at Ben's hands 5 years prior. It has been revealed by Dwayne McDuffie that this was intentional. Some time after, Vilgax returns to his usual size.
Vilgax returns in The Secret of Chromastone searching for Tetrax Shard, who had stolen back the crystal Vilgax used to destroy Petropia (which Tetrax had originally sold to Vilgax). Tetrax had discovered (unknown to neither him, nor Vilgax, at the time of the destruction of Petropia) that the crystal serves as a back-up for Petropia and its people. Vilgax tracks Tetrax to Earth and demands he turn over the crystal he stole, only to discover that Tetrax had given it to a freed Chromastone in order to restore Petropia (mistakenly revealed by Kevin). Vilgax leaves Earth and travels to Sugilite's location only to discover the newly restored Petropia. Outraged that "his crystal" was stolen to revive a "dead world" (one he destroyed), Vilgax beats Sugilite (who he compares to little more than a common thief). Sugilite begs Vilgax to let him revive the Petrosapiens and pleads for mercy, but Vilgax reveals he has no mercy to give. Vilgax mercilessly beats the helpless Sugilite, until he is confronted by Ben's Team and an angry Tetrax. Vilgax uses his shield to stop Tetrax's projectiles and then removes the "Petropian backup crystal" from Sugilite's head only to discover its energy had been used up. Seeing that the crystal was no longer useful, Vilgax throws it away and leaves Petropia (seeing it as nothing more than a lifeless planet and no threat to him) in disappointment. However unknown to Vilgax, Sugilite created a second backup crystal which is used by Ben to restore the planet's population. Tetrax later tells Ben he plans to settle the score with Vilgax, but Ben wonders how, given Vilgax's current invulnerability, he'll be able to do so. Vilgax returns to his home on Vilgaxia and is outraged to find out he had caught Ben's cold. The episode ends with Psyphon handing Vilgax a tissue.
Vilgax reappears in the series finale The Final Battle, wherein he teams up with Albedo, claiming he just wants to kill Ben Tennyson and will let the Omnitrix go to Albedo so he can regain his Galvan form. Though the plan is successful, Ben escapes thanks to Max's help, and Vilgax ultimately betrays Albedo, taking him prisoner and keeping the Omnitrix for himself in order to give its powers to his army of Bioids (robots synchronized with the Omnitrix for the purpose of assuming the alien form selected from the device).
Ben confronts Vilgax again and activates a lessened form of the Omnitrix's self-destruct mode (one that will destroy the device itself, without destroying the Universe along with it), hoping Vilgax will give it over before it detonates. Vilgax doesn't take his threat seriously however, allowing the Omnitrix to detonate. Enraged, Vilgax programs his ship to crash into Bellwood and attacks Ben and the others. Ben then frees Albedo and forces him to give up the Ultimatrix (which Ben then equips himself with). While Ben fights Vilgax as Ultimate Swampfire, Max and Gwen successfully cause the ship to crash in the ocean before reaching Bellwood. Now in the water, Vilgax reveals his "true form", transforming into a giant monstrous, octopus-like creature. He intends to swallow Ben, but the hero escapes, leaving Vilgax behind as his ship explodes. However, Ben, knowing that Vilgax has survived far worse, suspects that he may return.