Professor Clockwise is in his lab making the final adjustments to his time travelling device, but a large shadow creeps up behind him. Meanwhile his son Callum "Rascal" Clockwise is walking through a secret route under the house to get to his father's lab when suddenly the lights go out and an alarm sounds. Rascal rushes down to see the problem, but to his horror two aliens in spacecraft appear and chase him down the corridor.
Rascal finally makes it to his father's lab by going through the safe door entrance. He sees Chronon the evil master of time torturing his dad and holding him at gunpoint with another of his dad's inventions called the "Bubble Gun", but the villain accidentally activates the controls for the time machine and he and the Professor are sucked into the portal. The Bubble Gun manages to be released from the portal and lands at Rascal's feet, he picks it up, vowing to save his dad.
Rascal chases the two through time, going through the medieval Castle Hackalott, the Aztec Temple at Chichimeca, the lost city of Atlantis, the Jolly Raider pirate ship and the western town of Dodgy City in both past and present forms and fighting Chronon in each area's future. Afterwards Rascal travels to Chronon's lair in the Corridors of Time where, after defeating its guardians brought from each of the other time periods, he successfully defeats Chronon and rescues his dad. After escaping using another time portal, Rascal and his dad safely return home, leaving the portal to shatter and trap Chronon in interdimensional time forever.