Season 1 - Episode Guide

Five years ago, Ben Tennyson faces off with a new enemy,a red Galvanic Mechamorph, Malware. Five years later, Kevin and Gwen leave when Gwen takes early enrollment in an Ivy League college, and Kevin moves to be near her. Ben is forced to fight crime alone, but Grandpa Max (Magister Tennyson – the commander of the Earth-base's Plumbers) gives him a new partner, rookie Plumber Rook Blonko. Ben and Rook end up in their first team-up when Mr. Baumann's store is targeted for destruction by three alien criminals (Bubble Helmet, Fistina, and Liam) as part of their protection racket. An intergalactic hunter named Khyber watches Ben from the shadows.

After stopping Bubble Helmet, Fistina, and Liam from blowing up Mr. Baumann's superstore, Ben and Rook discover an underground alien city named Undertown where they discover that Psyphon is behind the protection racket. At the same time, Khyber sends his pet in the form of Buglizard to hunt Ben.

Ben meets an alien con artist named Professor Blarney T. Hokestar whose miracle elixir is extracted from a small alien called a Screegit that is kept in his lab. When a Florauna activist named Pax convinces Ben to help him free the small alien from Hokestar's lab, chaos ensues when the nitrogen in Earth's atmosphere turns the exposed Screegit into a giant, acid-spitting monster with Ben having to keep it from wrecking the city.

Dr. Animo has escaped his Plumber prison, and Ben and Rook must track him down before he transforms the world into his personal mutant ant farm.

Argit and the Vreedle Brothers are fighting for possession of a doomsday device. Ben uses the almighty Alien X's godly abilities to fully recreate the universe.

Ben and Rook come across elastic, hot-blooded aliens that plan to activate a volcano with a nuclear bomb engine. Ben later falls for a female alien named Esther.

While Ben is trapped in Khyber's ship, Khyber tells Ben that he needs different alien DNA to complete the evil incomplete version of the Omnitrix the Nemetrix he also reveals that Dr. Psychobos assigned him to hunt down various species for DNA to transfer it to the Nemetrix and also tells Ben that the reason Dr. Psychobos is creating an evil Omnitrix is because of the orders from Malware. After Ben breaks free, a brawl breaks out leaving Khyber the victor.

Just when it seems Ben is finished, Rook breaks in and saves Ben the duo then reveals to Khyber that they orchestrated the whole "fight" at Undertown and Ben only let Khyber capture him so he can lead them to his ship. After a long fight Ben and Rook accidentally crash Khyber's ship eliminating the DNA to complete the Nemetrix, Khyber and his Dog emerge unharmed as Malware and Dr. Psychobos arrive.