Season 2 - Episode Guide

While Khyber struggles to control his dog's transformations, Dr. Psychobos tells Malware that he will need a part of the Omnitrix to fix it. This causes Dr. Psychobos to infiltrate the Plumbers' base on Earth and steal a part from Ben's Omnitrix causing it to malfunction. The malfunctioning of the Omnitrix causes its powers to leak into Psyphon, Bubble Helmet, Fistina, and Liam giving them abilities very similar to the Omnitrix aliens.

Gwen and Kevin pay Ben a surprise visit; a Tetramand princess and her father's fleet of warships threaten the Earth.

Ben and Rook must stop Trumbipulor from gaining absolute power (which turned out to be peanuts since they can increase the size of Trumbipulor's kind). Yet the main plot occurs when Blukic and Driba set out to find a Mr. Smoothy's after seeing an advertisement for their new grasshopper smoothies and have many misadventures along the way with one of them tying into fighting Trumbipulor's robotic rats.

Ben and Rook are attacked by Khyber and his dog (which can now transform at will without Khyber's whistling) at the Old Bellwood Days Festival. In a flashback, it is also revealed how Malware had obtained his current mutated Galvanic Mechamorph form.

An old rival of Ben Tennyson named Billy Billions turns Ben and Rook into kids again while bringing Dimension 12 robots to Earth and controlling them.

Ben and Rook visit Rook's family on Revonnah during the Amber Ogia harvest. Meanwhile, Fistrick trains the planet's local rodents called the Muroids to steal the Amber Ogia as fuel for the planet-destroying satellite in his possession.

Eon returns and switches Ben's mind with his younger self as part of a plot to take over the timelines. It's up to Paradox, and the two Gwens from the past and present, to help the Bens' regain their rightful minds and help to defeat Eon.

Following Ben helping Grandpa Max defeat Liam, Ben takes Blukic and Driba to look for the 23rd Mr. Smoothy restaurant. After, Ben, Blukic, and Driba enter the 23rd Mr. Smoothy restaurant that keeps disappearing, they find it run by Professor Blarney T. Hokestar who is using a dimensional device to move the restaurant to different dimensions. In one dimension, Ben meets an alternate version of himself who is very rich, names his aliens differently and has lost his beloved Grandpa Max.

After Ben accidentally destroyed Mr. Baumann's car during his fight with Psyphon's minion, Thunderpig, Mr. Baumann orders Ben to make deliveries for him without using the Omnitrix. When Ben unknowingly gets the Dwarf Star (a massive power source that was going to be sold at Psyphon's auction) in his possession, Ben must fight off Pysphon, Fistina, Zombozo, Trumbipular, the Vreedle Brothers, Fistrick, Vulkanus, Sunder, and Seebik to keep them from getting absolute power.