During the events of the two previous games, Clank is kidnapped by the mysterious Zoni, led by the evil mastermind Dr. Nefarious, leaving Ratchet feeling all alone in the gigantic universe. Along with Captain Quark and Talwyn, he sets out on a quest to save Clank from Nefarious' clutches. Along the way he discovers the truth about his Lombax past and the secrets of time held within the Great Clock.
The gameplay is the same as in the rest of the puzzle-solving platformers of the series. Ratchet travels to different planets, smashing boxes for bolts and upgrading the various weapons in his arsenal, whilst defeating enemies and using gadgets such as hoverboots and the slingshot.
The game features some new gameplay mechanics however, such as space flying and the ability to manipulate time. Ratchet can fly his ship freely through space, allowing him to stop on moons and acquire the special items that they hold. Clank now has the power to manipulate time: with a new staff he is able to rewind time and record his actions to aid him tricking bad guys and solving puzzles.