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After the events of Ultimate Alien, Ben is left to be a sole hero after Gwen and Kevin leave for college. However, Grandpa Max has other plans. He teams Ben up with a Plumber rookie just out of training, Rook Blonko. Ben does not want to have a partner and tries refusing Rook, but in vain. Setting their differences aside, the two soon learn to work as a team and look out for each other.
11 years old Ben: Ben as Four Arms fought Malware. While at first it appeared that Ben was winning, Malware managed to grab the Omnitrix and forced Ben to revert back to human. 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 used his energy absorbing and redirecting powers to quickly defeat Malware.
16 years old Ben Ben and his team track down and capture Zombozo who has stolen a human brain from the Bellwood Brain bank. The team is separated when Gwen Tennyson goes off to college the next day and Kevin Levin decides to join her. Although the departure is saddening Ben feels he's ready to work alone now. Later that day Ben investigates a explosion at Pakmar's Toilet emporium.
In the ruins of the store Ben fights a Crabdozer as Spidermonkey and narrowly avoids getting eaten as the beast suddenly retreats. Concluding that if somebody is bombing Alien businesses then they may hit Mr. Baumann's grocery, which he concludes is true. A trio of thugs come in to collect their protection Money and does battle with Ben as Cannonbolt.
During the fight one of Mr. Bauman's customer's reveals himself as Rook Blonko, Ben's new partner from the Plumbers' Academy. Although Rook proves invaluable during the fight Ben is adamant that he doesn't need a partner, regardless the two end up working together to use Ben's latest alien form Bloxx to detonate the bomb safely, revealing Undertown which the two Plumbers chase the criminals into.
Thinking that he has won, the Megawhatt escapes the cup and duplicates. Ben remembers he has Feedback and turns into him. He sucks the energy out of the Megawhatts, which make them go to sleep.
Ben and Rook check out a mysterious ghost ship. Later on after meeting old enemies, Ben has to use Alien X to save the universe from a raging bomb. When Ben transformed back from Alien X, he gained a green and white jacket that had a hoodie, and a number 10 logo on it.
16 year old Ben: Ben is attacked by Khyber and his pet. He turns into Crashhopper to battle, but Khyber's pet turns into Mucilator and falls on Crashhopper, so Ben turns into Armodrillo and throws Mucilator.
Mucilator later turns into Slamworm and goes underground, attacking Armodrillo. Armodrillo turns into Heatblast and chases after Khyber, but meets a surprise attack by Crabdozer. Heatblast tries to turn into Humungousaur, but becomes a new alien named Ball Weevil. At first Ben didn't know how to use Ball Weevil's powers, but then spits a ball and rolls around uncontrollably before seeing that the ball can explode. Crabdozer counters this by turning into Terroranchula.
Ball Weevil flees, but Khyber defeats him by redirecting one of his balls. Ball Weevil reverts back into Ben and falls down unconscious.
Ben eventually discovers from Khyber that Malware is the true threat.
16 year old Ben regains Feedback.