The plot follows on from Ben 10: Alien Force; set one year after the events of the last series. The Omnitrix has been destroyed, and Ben must learn to master the secrets of the new Ultimatrix, a gauntlet-like version of the old Omnitrix that not only gives him access to all of his original powers and abilities, but also allows him to evolve his alien forms into even stronger and more powerful versions (called "ultimate forms").
However, in the premiere episode, "Fame", a young ten-year-old fan named Jimmy Jones deduces Ben's secret identity and reveals it to the world. Ben becomes an overnight celebrity, hailed by kids as a hero but distrusted by most adults as a possible threat. With Gwen, Kevin, Julie, and Grandpa Max still at his side, Ben continues to battle alien threats to the galaxy, including finding five aliens that were attacked and kidnapped by an Osmosian villain named Aggregor. Their names were Bivalvan, Galapegus, P'andor, Andreas, and Ra'ad. After Aggregor captured and fused with all five aliens, he began searching for the Map of Infinity to go to the Forge of Creation and absorb the vastly limitless God/cosmic-like powers of Celestialsapiens.
Later Kevin becomes once again a main antagonist to the Ben 10 series after he is forced to absorb energy from the Ultimatrix and goes insane with tremendous energy and power, but is shown that he does still have a good human heart, and still does care, and that he has not gone completely evil. Kevin is eventually returned to normal and Aggregor's actions are reversed.
The second season features more self-contained stories rather than employing an overall storyline, although a real storyline is developing with the appearance of the mysterious, but dangerous Sir George and the extra-dimensional demon called "Diagon".
After the defeat of Vilgax who absorbed the enormous abilities and powers of Diagon to become even stronger and more powerful, Azmuth appears to ask Ben to give his sword and the Ultimatrix back, giving Ben the new-and-improved and greatly modified version of the Omnitrix.