In Ben 10: Ultimate Alien, sixteen-year-old Ben's secret identity is revealed to the world and he's now a megastar superhero loved all over by kids. This series features Ben's new car, the DX Mark 10 a heavily modified Mazda RX-8, which marked its first appearance in Ben 10: Alien Swarm, the car being gifted reluctantly by Kevin.

He is also seen with Julie, who now shares a considerably stronger bond with; the two help their team from time to time. He and Julie also share their first on-screen kiss at end of the episode Fame, though it was merely a kiss on the cheek. He gained a lot of confidence after Julie kissed him, and Ben appeared to be utterly shocked at Julie kissing him on the cheek. Ben and Kevin are now true friends, not rivals.

Ben is now armed with an enhanced, upgraded version of the Omnitrix, the Ultimatrix, which evolves his aliens into their Ultimate Forms (as he calls them), and also has every alien he has ever transformed into, though at the moment, Ben has yet to either transform into or re-unlock all of them (His future self Ben 10,000 has unlocked all of the aliens he has ever transformed into up until now, with a few new ones just to annoy Azmuth). He is now also on good terms with his old school bullies, Cash and J.T.

The series introduces two new enemies for Ben's rogue gallery: nasty news reporter Will Harangue, who sees Ben as a public threat (he heavily represents J. Jonah Jameson from the Spider-Man universe), and a villainous Osmosian named Aggregor, whose sinister plan involves draining the powers of five powerful aliens from the Andromeda Galaxy to make himself the most powerful being in the galaxy. Interestingly, these five aliens also provide Ben with his five newest alien forms.

After Ben scanned Ra'ad, he now has a total of 1,000,910 genetic samples in the Codon Stream. After Kevin was mutated by absorbing the Ultimatrix's Energy Core and lost his sanity again, he successfully defeated Aggregor with help from Young Ben. Kevin was finally cured in Absolute Power: Part 2 with help from Darkstar and what was left of the Dominus Librium. After rescuing Baz-l in Eye of the Beholder, he and Julie become a couple again as he promises to be a better boyfriend.

He then faced the Lucubra, a creature from an alternate dimension. He was told to beware it by a man named Old George and by Paradox in Ben 10,000 Returns.

In Solitary Alignment, he learns about Azmuth's creation, the Ascalon, the sword that is wielded by Sir George and is told of how Sir George obtained the sword. Ben struck up a deal with Sir George, that if he is unable to slay Dagon, then he will take the sword and attempt to defeat Dagon.

In The Ultimate Enemy: Part 1 and Part 2, Ben and his team go to the final battle between Dagon and Vilgax. Dagon turns every human on Earth into an Esoterica and fought Ben and George. Dagon's seal was broken, and he appeared in the human world. Dagon was too strong for even Ultimate Way Big to stand against, and Sir George was turned to dust when trying to fight him. Vilgax used Psyphon's device to drain Dagon's very essence to transfer his power to him. The team took the sword Ascalon and fled to the Mount Rushmore Plumber base. Vilgax forced his way inside and knocked Gwen and Kevin unconscious. Vilgax boasted about how he planned to fight another of Ben's Ultimatrix transformations; Ben decided to use a different means to fight him, Ascalon. He uses the sword to subdue Vilgax and absorb Dagon's power from him.

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Ben wearing the new Omnitrix and with his team

Ben may have won the battle, but he is tempted by Vilgax. Since he has the power of the Ultimatrix, Ascalon, and Dagon at his fingertips, he could fulfill his desire for peace and justice with a simple thought to destroy all evil. Ben considers this at first, but Gwen, Kevin, and even Julie try to talk him out of it. It seemed that he wouldn't give up until he uses the power to turn every Esoterica on Earth back to normal, and all the free will that goes with it. He relinquishes the sword, saying that Azmuth was right, it is too much power for anyone to have. Azmuth appears and Ben gives the sword back to him. He asks for the Ultimatrix too and gives Ben a new Omnitrix, one that he has been working on for six years since he found it. Ben asks for its Master Control, to which Azmuth replies perhaps for his 18th birthday.

He appears in the Generator Rex episode Heroes United in order to help Rex deal with a "common threat" which was the sentient Alpha nanite. His appearance changed based on the series art style, becoming sleeker and more mature.

Ben was at a celebrity gig when a strange storm picked him up and dumped him into Rex's world, where he mistook Rex Salazar for an alien attempting to destroy Bellwood. However, he was also mistaken for an EVO, who Rex tried to cure, but both found that they were not what the other thought they were.

"Captured", Ben was taken back to Rex's with an unconscious Agent Six following a battle with an unknown enemy he had been chasing through the storm. While in the base, Ben learned of what was going on in that world, becoming confused by some facts, but generally grasping things are not going good.

Deciding to team up with Rex, Ben met Caesar, Rex' brother and learned that he had banished the Alpha nanite to the Null Void, thinking it was an empty dimension when in reality it's a prison for alien criminals.

However, Alpha had returned and planned, not to mention succeeded, to absorb Rex's Omega 1 Nanite to finally create a body that could sustain itself, in addition to that it copied the Ultimatrix for extra firepower. Ben transformed into Upgrade and fused with Rex, allowing them to use more powerful versions of Rex's weapons to beat down Alpha. With Caesar's help, Ben entered the Null Void as a stop on the way back home, using Murk Upchuck to dump Alpha into the Null Void.

16-year-old Ben also appears in a flashback in Rules of Engagement where he is in his room playing Sumo Slammers. He starts talking to Julie but he also starts yelling out to the game at the same time. Julie, believing Ben broke up with her, turns off her phone and the flashback ends.

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