The sequel Ben 10: Alien Force continues Ben's adventures five years after the original series. At some point between the two shows, Ben, now fifteen years old, had succeeded in removing the Omnitrix through an unknown but difficult process, and chose to retire from his superhero career in order to have a normal teenage life, though he kept the deactivated Omnitrix as a souvenir. He then grew up into a slightly more mature teenager, losing his unpopular status at school and becoming a skilled soccer player.
However, after winning his latest match, Ben finds that his Grandpa Max had mysteriously disappeared while investigating what Magister Labrid calls "an alien conspiracy with Earth in the middle" leaving only an enigmatic holographic message for Ben. Despite Gwen's doubts, Ben decided to use the Omnitrix again in order to find Max. When he reattached the Omnitrix, it recalibrated itself, taking on a new, more watch-like appearance and providing him with a new, more exotic set of alien transformations. These ten new aliens were more powerful than his original ten.
While helping the Alien Plumber Magister Labrid investigate Max's disappearance, Ben and Gwen encounter Kevin, now a weapons dealer, brokering a deal between the DNAliens and the Forever Knights. Kevin attempted to attack Ben, still bitter after all his past defeats against him and his eventual imprisonment in the Null Void, but was again easily defeated after fighting Ben's new alien Swampfire and caught by Labrid. He then agreed to help them, hoping to get back the money he lost during the deal. Eventually, after an altercation with the Forever Knights and Labrid sacrificing his life to save Kevin's, Ben, Gwen, and Kevin start working together as a team to face the Highbreed's expected invasion on Earth.
At the same time, Ben developed mutual feelings for Julie Yamamoto, an Asian/American girl from his school. Though he was initially afraid of developing a relationship with her, fearing she'll reject him if she found out about the Omnitrix, he was eventually pushed by Gwen into taking her to a date at the Pier. The date, however, went wrong when a Galvanic Mechamorph symbiote (later named Ship) started attacking Ben in an attempt to get his attention. This incident eventually forced Ben to reveal his powers to Julie, but to his surprise, she didn't reject him, even calling the Omnitrix "cool." The two eventually continued dating, while Ship became Julie's pet.
Ben also discovers that himself, his cousin Gwen, his father Carl, and Uncle Frank have alien heritage from an alien species called Anodites, though it is a dormant gene within him and he does not have the same potential that Gwen does. This is proven in the episode “Ben 10,000 Returns” when he magically produced an energy shield to block Eon's aging ray.
At some point, Ben received a visit from a mysterious clone-like being of himself. The clone introduced himself as Albedo, a Galvan, stating he was the true creator of the Omnitrix and that Azmuth was a liar. He asked Ben to hand over the Omnitrix, stating he was trapped in Ben's body since his DNA had become the Omnitrix Default and needed Ben's Omnitrix to override the device's programming. When Ben refused, he turned violent and attempted to take it by force. After two clashes between them, Azmuth appeared and revealed that Albedo was actually his assistant, who was untrusting of Ben and had attempted to make his own Omnitrix. As a punishment for his arrogant act of rebellion, Azmuth removed Albedo's Omnitrix's central component (the Core), leaving him trapped in a damaged, photo-negative version of Ben's human form, and sent him to a Null Void prison.
During one mission, Ben was accidentally sent through a teleportation device with the Highbreed commander Reinrassic III, causing both of them to be trapped on the hostile planet Turrawuste and forcing them to work together in order to find a way back to their respective homeworlds. Though initially displaying the usual racist Highbreed's behaviours, Reinrassic slowly developed a friendship with Ben, and eventually lost his hand trying to save him from a local vicious life form. After Ben heals his hand as Swampfire, they eventually reach the teleportation gate, but Reinrassic III chose to self-exile himself on Turrawuste, as he believed his friendship with Ben had corrupted him in the eyes of his people.
Ben eventually assembled a team, consisting of himself, Gwen, Kevin, Alan Albright, Professor Paradox, Julie, Ship, Cooper, Azmuth, and a briefly reformed Darkstar for a final attack on the Highbreed's hideout in Los Soledad in order to prevent the Hyperspace Jumpgate located there from being activated, which would unleash the Highbreed fleet on Earth. Despite help from Max and the Plumbers' helpers, they failed to prevent the arrival of the fleet. Ben then went with Gwen, Azmuth, and Kevin aboard Ship through the Jumpgate to the Highbreed homeworld. He then discovered the Highbreed were actually trying to exterminate every known sentient being in the Milky Way galaxy because they were slowly dying out and, as stated by Azmuth, their belief in purity among their kind had led to inbreeding, a loss of disease resistance, and finally sterility. Ben, as Humungousaur (which he used to break out of a holding cell), asked if the Omnitrix can repair the genetic damage to all of the Highbreed; the device replied that it can, but such an action would require all of its available power. After turning Ben back to his normal self, it then charged up and released a powerful energy/DNA wave that infused all the Highbreeds with alien DNA from the Omnitrix's genetic database, thereby repairing their genetic damage in the process and saving them from total extinction. Though they were initially disgusted by this (and contemplated mass suicide as their only honourable act because of the change), Reinrassic III then re-appeared from his exile, and showed them how this "genetic impurity" was giving them a second chance at life. Realising he was right, his comrades named him Highbreed Supreme and he ended the war, thereby bringing peace to the galaxy once more.
After his successful attempt at ending the Highbreed Conspiracy/Conflict on Earth, Ben grew famous and was celebrated as a hero throughout the whole galaxy, and received awards from various Alien Ambassadors (e.g. Lukik). This caused him to eventually relax and return to his immature and somewhat cocky attitude from the original series, much to Gwen's and Kevin's chagrin. When he had to face the return of his old nemesis Vilgax, Ben attempted, with help from Kevin, to hack the Omnitrix in order to unlock the master control. This attempt went awry, releasing Goop, Chromastone, Spidermonkey, and Way Big from the Omnitrix as mindless, instinct-controlled creatures and causing Kevin to mutate for the second time. Worst of all, Ben loses Azmuth's trust. After reabsorbing the four aliens, Ben faced Vilgax and eventually defeated him as Diamondhead, though he temporarily lost Chromastone in the process.
Ben continued working as an honorary member of the Plumbers with Gwen and Kevin, with Max providing them with various missions throughout the third season of the series (Inferno and Fool's Gold being examples). He also had to deal with Vilgax, who continued trying to find ways to have his revenge on him (e.g. attacking Primus).
Eventually, Ben had to face a coalition of Vilgax and Albedo, the latter having stolen a prototype upgraded version of the Omnitrix, the Ultimatrix, from Azmuth's lab. The two of them successfully took Kevin and Gwen hostage, leading Ben to deliver the Omnitrix to Vilgax. However, Ben eventually was forced into activating the Omnitrix's self-destruct sequence, threatening Vilgax to let it explode if he didn't remove it. Vilgax mistook this for a bluff, and paid the price (the Omnitrix exploding with the force of a small bar of C-4 plastic explosive or half a stick of dynamite), causing Kevin to lose his old mutation in the process. However, Ben then forced the Ultimatrix off Albedo to fight Vilgax as Swampfire and then as Ultimate Swampfire. The galactic conqueror's ship then hit the Pacific Ocean just offshore from Bellwood, with Ben, Gwen, Kevin, and Max all escaping from it mere moments before its Fusion Drive exploded like a bomb.