One year after the original series, Ben, who (along with his cousin) is now 11-years old, continues to live in Bellwood and use the Omnitrix to help people and defeat any of the terrestrial and extraterrestrial threats that his team encounters as well as goes on weekend trips with them. Ben also unlocks several new alien forms during this time.
In A Jolt from the Past, Ben as Stinkfly fought a Megawhatt. After reverting back into normal, he grabs a Mr. Smoothy cup and traps the Megawhatt in it. However, the Megawhatt escapes the cup and duplicates. Ben transforms into Feedback and absorbs the energy out of the Megawhatts, which make them go to sleep.
In Trouble Helix, the Tennysons meet Malware, an incomplete Galvanic Mechamorph accidentally created by Azmuth, who loses his patience and kidnaps Albedo, Azmuth's assistant, to complete himself. Eventually, he is turned into a more powerful form, only to be defeated by Diamondhead.
In The More Things Change: Part 1, Ben as Four Arms fought Malware. While at first it appeared that Four Arms was winning, Malware managed to grab the Omnitrix and forced Four Arms to revert back into Ben. Malware confronted Ben and taunted him about his defeat, which allowed just enough time for the Omnitrix to activate again. Ben transformed into Feedback and quickly defeated Malware. During the fight (as revealed later in both Of Predators and Prey: Part 1 and Of Predators and Prey: Part 2), Malware had successfully created a blueprint by absorbing Omnitrix.
In Malefactor, the team visit the Plumber base in Mt. Rushmore. There, they are attacked by Malware who is seemingly defeated by a Tachyon Cannon. However this just transforms him into a more powerful version of him. He gets defeated, although, he was just a distraction so that Khyber can sample a rare Psycholeopterran.
In Ben Again, while battling Eon, 11-year old Ben's mind gets switched with his 16-year old self. As 16-year old Ben, he finds the clues laid down by the 16-year old Ben who is inhabiting 11-year old Ben's body. 11-year old Ben manages to get his body back and defeat Eon.
In Showdown: Part 1, Ben transforms into Feedback many times to defeat the Violet Offenders, somehow stop a fire, and practice his powers. Due to Ben's constant use of Feedback, Azmuth comes to Earth to warn Ben that this is affecting his other transformations. Ignoring him, Ben transforms into Feedback again and prepares to fight Malware who has returned. This results in Feedback being destroyed and Malware being seemingly killed when he is overloaded by the Omnitrix's energy.
In Showdown: Part 2, Ben and Gwen exit the Rust Bucket when Max brings them back to Ben's house. Ben is depressed and upset about losing Feedback. Azmuth arrives and explains that Ben never learnt anything from winning and that losing Feedback was hard for him. Ben says that Feedback was like a part of him but Azmuth says that Ben could learn something from losing Feedback. Ben eventually forgives his future self and this allows 16-year old Ben to regain Feedback.
In The Vengers, Ben saves the people from an exploding building and captures Kangaroo Kommando as XLR8. With this Ben makes new enemies, in the forms of Captain Nemesis who sees him as a rival and Will Harangue who sees him as a vigilante.
In Bengeance is Mine, Ben is captured and tied upside down in ropes by Vilgax in his ship. Vilgax then threatens to feed Ben to his numerous Squid Monsters, but Ben breaks free and transforms into XLR8. XLR8 tried to battle Vilgax, but he was grabbed by a Squid Monster. The flashback is cut short here, so it is unknown how Ben landed up in this situation or how he got out of it.
In Evil's Encore, the team encounters and defeats Dr. Animo again during their visit at the Plumber base at Mt. Rushmore after he managed to take control of the base to use the Plumber satellite network in order to spread his mutation ray over Earth.
In Weapon XI: Part 2, the team fights Kevin again, who was associated with the Amalgam Kids at the time. Kevin once again absorbs the Omnitrix's energy and undergoes another mutation that causes him to transform into an alien hybrid that consists of the other 10 aliens Ben unlocked in the original series. After Kevin trapped everyone in vines and planned to kill them, Argit managed to knock out Kevin. Afterwards, Kevin, Argit, and the Amalgam Kids return back into the Null Void.
In From Hedorium to Eternity, Ben, Gwen, Lucy, Cooper and Jonesy meet Kevin underground and together stop Zs'Skayr and his Ectonurite minions from taking over the planet. Ben learns to trust Kevin but he once again gets stuck in the Null Void. Ben and Gwen had never encountered him again until four years later, when they have developed into teenagers.
At some point later, for unknown reasons, Ben removes the Omnitrix and never wears it again for the next four years.