After parting ways with Gwen and Kevin, Ben is assigned a new alien partner named Rook Blanko. Meanwhile, Khyber the Hunstman targets Ben as his next prey.

Rook and Ben find a mysterious alien city under Bellwood after stopping 3 alien crooks: Liam, Fistina, and Bubble Helmet from blowing up Mr. Baumann's superstore in a protection racket.

The Megawhatts that Ben fought in his youth seek his help when they are being used as a power source for the villain Fistrick.

Infiltrating the Plumbers' base, Khyber uploads footage of young Ben's encounter with a corrupted Mechomorph named Malware.

Ben and Rook must stop a giant rampaging alien from destroying Bellwood while dealing with a peace-loving alien-rights activist who doesn't want it hurt.

Ben and Rook attempt to stop Dr Animo and his giant ants.

When Ben and Rook investigate a mysterious alien ghost ship, they discover that Argit and the Vreedle Brothers are fighting for possession of a doomsday device.

It is revealed that during a fight with Eleven-Year Old Ben Tennyson, Malware touched the Omnitrix symbol on Four Arms. After the battle, he went to Dr. Psychobos and made him create a prototype Omnitrix, the Nemetrix. Back in the present, after a heated argument, Ben and Rook go their separate ways, giving Khyber his best chance to capture Ben.

While 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.