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In a future where an adult Gwen Tennyson is president and the world is being taken over by the alien horde known as the Xerge, a disillusioned Ben 10000 is called out of retirement to recruit his 10-year old version from the past.

When Ben meets a young Generator Rex on the run from a hostile Providence, he must work through a series of misunderstandings, and defeat the dark wizard Hex in order to save the world from a malfunctioning Omnitrix infecting the world's human population with alien DNA.

The Tennysons are attacked by a villainous dimension-hopping Omni-alien known only as Alien X. With help from a parallel universe version of Max, they bring multiple alternate Bens and Gwens together to form an alien hero army and combat this threat.