Gwen's older brother, Ken, is suddenly missing. As they look, they encounter a surprise leading to a shocking secret from the DNAliens.

A time experiment in the 1950s sends a bizarre monster to Ben's time. Now Ben, Gwen, and Kevin must team up with Paradox, a time traveling hero, to face off against the unstoppable creature.

When Ben's parents discover his ability to turn into aliens, they forbid him from using the Omnitrix and later ground him from using it again. Eventually Gwen is grounded too leaving Kevin to stop the DNAliens.

After Gwen receives an S.O.S. from Helen, Ben must go into the Null Void to save her and Manny. Once there, he must find The Wrench in order to stop D'Void, who happens to be Ben's old enemy Dr. Animo