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.

Ben must battle mad scientist Dr. Animo, who plans to destroy Washington D.C. by bringing dinosaurs to life.

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 thieves, who are arousing the Krakken by trying to steal its eggs.

Grandpa, Gwen and Ben visit an elderly relative only to find that her retirement community has been overrun by a group of shape-shifting aliens!

Ben will find himself facing his toughest challenge yet, when Vilgax sends out three alien bounty hunters: the crustacean-like Kraab, the mechanical assassin Sixsix, and the mysterious Tetrax (credited as Hoverboard) - to recover the Omnitrix. He soon learns that there's more than one way to defeat an enemy, and that things are not always what they seem.

Ben's prank backfires when he releases a Megawhatt, a destructive monster made of electrical energy.