The second season sees the team facing new challenges, including the introduction of the Transylians, a species of alien warlords. The season also explores the origins of the Omnitrix, a powerful device that Ben uses to transform into different alien creatures.

By the final frame of the last episode (the prelude to Ultimate Alien ), Ben is no longer the boy who wanted the Omnitrix. The Omnitrix is a burden he chooses to carry. The deep story of Ben 10: Alien Force is this:

The two-part finale isn't about beating Vilgax. It’s about Ben choosing who he is. He loses the Omnitrix. He gets it back. He beats the bad guy. But the deep story is in the quiet scene after the explosion: Ben, Gwen, and Kevin standing in the rubble of Bellwood, exhausted, covered in dust, not cheering. Gwen asks, "What now?" Ben looks at the rebuilt Omnitrix—now a sleek, black, adult watch—and says, "We keep going."