Ben and his alien hero personas must battle Dr. Animo a crazed mad scientist bent on revenge and armed with the DNA altering Transmorpher device. Animo uses the Transmorpher to mutate normal animals into monsterous, and then to reanimate dinosaurs that run rampant in Washington D.C. Meanwhile, Ben discovers being a hero is not just about getting rewards for your good deeds.

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 (the Omintrix Prototype) that has been jettisoned from alien spacecraft high above the earth. When the prototype attaches itself to Ben's wrist, he discovers that it allows him to become any one of Ten Aliens. Ben's first test as a hero comes early as Vilgax (Season #1's main villain) sends Mecharoids to procure the prototype.

While stopped at a lakefront campsite, Ben has a chance encounter with a Loch Ness type sea monster called a Krakken. Eventually, Ben discovers the true threat - the evil poacher Jonas and his high-tech deep water theives – who are stirring up the Krakken by trying to steal its eggs .

Grandpa, Gwen and Ben visit an old maid relative only to find that her retirement community has been overtaken by a shapeshifting aliens called Limax. The Limax are systematically gathering the elder population for transport back to its home planet to use as a food source. Ben must use his alien heroes to defeat the Limax and rescue not only his matronly aunt, but Grandpa Max as well.

Ben finds himself hunted down by three alien bounty hunters – the crustacean-like Krabb, the mechanical assassin Sixsix and the mysterious Hoverboard - hired by Vilgax to procure the prototype watch. The experienced and powerful mercenaries provide Ben's alien heroes with their first true challenges. Fortunately, Hoverboard is a double agent working on the side of good to make sure the Omnitrix doesn't wind up in the wrong hands. Unfortunately, he is not too pleased that Ben treats the most powerful weapon in the galaxy as a play toy.

When Ben can’t resist messing with the Worlds largest rubber band at a cheesy roadside tourist trap town, he accidentally releases Megawhatts, mischievous and destructive creatures made of electrical energy with the power to warp reality to their own sinister prankish delight, that were living inside. Ben must then use his alien hero personas and his own practical joke-loving ideas to recapture the Megawhatts before they can threaten a major population center.