While battling Dr. Animo Ben accidentally causes the self-destruct protocol on the Omnitrix. This alerts Tetrax who travels to Earth and takes Ben with him to find the creator to help stop the countdown. Despite wanting to go Gwen and Grandpa Max are not allowed to come so out their enemies won’t recognize them. Nevertheless Gwen sneaks on Board.
With the Equipment on board Tetrax uses the equipment on board of the ship to find the Omnitrix’s creator the Legendary Azmuth and go to Incarcecon the Prison Planet to find him.
After Freeing Myaxx a member of Vilgax’s species they discover that she isn’t Azmuth but rather his assistant who erased his genetic signature in revenge for not giving her some credit in the Omnitrix’s creation.
While Myaxx is unable to stop the self-destruct she does tell him that she knows how to find Azmuth and leads him to where he is hiding…Xenon.
While on the Journey there, Ben finds out that the self-destruct will destroy most of the Universe including Earth and that the more he transforms the more he speeds up the clock.
Vilgax has picked up the self-destruct signal as well and follows them. Along the way he picks up Sixsix who escaped Incarcecon.
While the team goes to Azmuth they are attacked by Vilgax.
Ben successfully repels the attack though Gluto is killed and the ship is really damaged and crash lands on Azmuth’s homeworld. While tracing him they are attacked by the Florauna and Gwen is killed in the attack which depresses Ben who blames himself.
As they travel down towards Azmuth’s lair, Tetrax tells Ben his origins and how his greed had cost him his planet and his people.
They find Azmuth who refuses to help. They soon find out that he is a Galvan who doesn’t care if the Whole Universe is destroyed or not. He then says the Omnitrix was designed for peace and understanding and all the people who used it used it as a weapon and are the problem.
Vilgax having recovered from the battle earlier attacks Azmuth’s home. Gwen and Gluto reappear revealing that Gluto could regenerate from even the smallest blobs left and that he was on her and rescued her from the Florauna.
Ben’s actions make Azmuth change his mind who repairs the Omnitrix and gives Ben access to Way Big a gigantic alien the size of a Skyscraper.
After defeating Vilgax(by throwing him into Space), Ben offers to return the Omnitix to Azmuth who allows him to keep it. Azmuth then says he is the best person for it and that he doesn’t want the trouble it brings.
After being returned home by Tetrax(who gives him a replacement hoverboard) Ben goes with his family to fight the ‘zombies’ attacking the mall.