Average kid, ten year old Ben Tennyson, his Grandpa Max and his cousin Gwen's summer of adventure takes an odd turn when Ben discovers a watch like object that has been jettisoned from alien spacecraft high above the Earth.

Ben must fight Dr. Animo, a crazed scientist who has a DNA-altering device.

At a city, Ben, Gwen, and Grandpa Max are waiting outside a video game store to purchase the newly-released Sumo Slammer video game. Gwen and Grandpa Max go the book store, but when they return to check on him, Four Arms comes out of the store by force. They return to the RV, and find that Ben is already there. Gwen yells at Ben for what he's done, but he has no clue of what she's talking about. But as she gives direct evidence that Four Arms was attacking the city, Ben heads out to find the perpetrator, using the identity of his aliens to ruin his current reputation as a hero.

A terrorizing nightmare of Ghostfreak is half the trouble for an unnerved Ben, as a tour of an important academy that Gwen wishes to attend is disturbed by the uncanny alien's manifestations and the antics of Acid Breath, Frightwig, and Thumbskull.

While driving on a Florida highway, a bus of escaped felons rams into the RV. Ben transforms into Stinkfly (though not intentionally) and tries to stop them. With a little help from Grandpa's handy driving, and a magic spell from Gwen, the felons are put back in jail. On the news, the Tennyson's hear about purple lightning delaying a space shuttle launch. Remembering the lightning from the encounter with the werewolf and mummy aliens, they head to Cape Canaveral. At the Space Center, Ben comes under attack by the werewolf and mummy aliens, and new Frankenstein alien. However, why is the purple lightning occurring, and what ties does it have to an old "friend"?

While snowmobiling, two guys accidentally release an alien named Xylene from a strange container. At a park, Ben (as Wildmutt) steals Gwen's kite, so she casts a spell to make dogs attracted to him. Grandpa Max seems sad to be in St. Louis since it is where he met his wife. Xylene attacks, and Grandpa Max comes to defend, only to recognize her. Xylene reveals that she came to find the Omnitrix since she lost it when Vilgax attacked her ship. While Grandpa Max and Xylene talk about the past, a robot emerges from the area where Xylene was and attacks Ben and Gwen. The mechadroid attacks twice, taking Grandpa Max with him. Now Ben must work with Xylene (to his dismay) to save Grandpa Max.

Two men try to carjack the Rustbucket while Grandpa Max is out. Fortunately, Ben is on the Rustbucket and the carjackers end up messing with Four Arms. But Grandpa Max doesn't believe Ben about this.

After being in contact with water from the Fountain of Youth, Grandpa Max and Ben are reverted to being kids again. Now, Gwen is left to take care of them while stopping Hex from finding the fountain's source.

Ben, Gwen, Cooper and Grandpa Max face their last battle ever against the villains they have encountered and they will battle to get the world's most powerful energy source.

The summer finally ends. Ben and Gwen have to go back to their normal lives. Grandpa Max tells Ben to keep the Omnitrix a secret from everyone, even his parents. Ben agrees, but Vilgax arrives and he'll stop at nothing to get the Omnitrix.