The Time Keepers have anticipated the arrival of Flynn and the Skylanders, seeking their help in discovering what causes time itself to go backwards repeatedly.
When the Tower of Time suddenly turns back time itself, Flynn encounters his past self and the two immediately become friends before returning to the present.
Once there, the main Time Keeper and the two Flynns discover that the local evil bird, Cluck, has taken over Clock Town with an army of Time Trolls after acquiring a new mechanical suit from them, making the Tower of Time his new home.
Despite the dangers surrounding Clocktown, the Skylanders managed to recover three colorful gears from Cluck's ancient nests, needed to enter the Tower of Time to stop the evil bird.
Once inside, they confronted Cluck in the Clock Tower and defeated him, destroying his mechanical armor. Cluck swears revenge as he clumsily flies out of the Tower of Time.
As time is properly restored, the present-day Flynn and the past Flynn separate to their respective time periods, agreeing that "the universe could only support so many awesome things at a time" and that they are both the best.
