Rook Blonko picks up Ben Tennyson from Undertown after he wrecks his Tenn-Speed doing tricks. A car accident leads the two Plumbers to crash in the nearby ditch where their vehicles are further wrecked by Exo-Skull tearing through them and into the wall behind them. In the process, an assortment of time beast eggs are revealed.
Ben turns into Feedback and Skurd produces a pair of Wildvine whips to fight Subdora, while Rook fights Exo-Skull. In the commotion, a Time Beast with the ability to age whatever it touches to dust appears and makes its way to the surface. Ignoring the two criminals, Feedback and Rook chase the beast to the surface where Feedback's electrical powers collide with the Time Beast's time powers. This leads to all of Bellwood being frozen in time.
Professor Paradox and Ben 10,000 arrive, realizing what has happened and reverse time back to the crash.Eon explains to Exo-Skull and Subdora that a nest of Time Beast eggs is hidden in the wall and assigns the two criminals to break it open and steal them. With the two Plumbers' accidental intervention, Eon is forced to modify his plans using his time powers to hatch one of the eggs into a full grown Time Beast.
Paradox and Ben 10,000 arrive on scene, assigning Ben and Rook to go after the Time Beast while they deal with the three villains. Eon and Paradox fight while Ben 10,000 makes use of Crashocker to fight off the two criminals. After Eon flees and the two lackeys are rendered unconscious, Paradox assigns Ben 10,000 the task of using UpRigg to build something useful out of the two destroyed vehicles.
Meanwhile, Ben and Rook once again follow the Time Beast to the surface, with Ben making use of Gravattackand Skurd creating the 'Bloxx Lobber' to shoot at her. The colliding time and gravity powers trigger a chain reaction that destroys the city. Paradox and Ben 10,000 arrive just in time on the newly built Time Cycles to save them by bringing them back to the time of the crash.
There, Paradox and the past and future Ben and Rook try to subdue Eon and the two criminals, though he still manages to hatch a Time Beast. The future Ben and Rook take the Time Cycles and go after the Beast while the past Ben and Rook fight Subdora and Exo-Skull. Meanwhile, Paradox and Ben 10,000 as Big Chuck fight Eon and his minions. The fight ends in a draw with Eon getting away with two eggs and the criminals.
Ben and Rook trap the Time Beast in nets and revert her back into an egg using the Time Cycles. Paradox and the others reunite, with Paradox stating that he has to take the past Ben and Rook back in time to 'close the loop' and take the place of the now current Ben and Rook as well as build the Time Cycles, which the two Plumbers keep. Meanwhile, Eon delivers the eggs to Maltruant, stating that he almost has everything he needs to complete his plot.