Secret Agent Clank has the character Clank from the Ratchet & Clank series taking the lead in this adventure. Ratchet is sent to prison, and it's up to Clank in his Secret Agent persona to save him and while he's at it, the entire universe! Ratchet is playable in prison and fights all of his worst enemies that he put behind bars. The series’ boastful hero Qwark tries to get in on the action and follows Clank around taking credit for his accomplishments. You get to play as Qwark and help him complete his exaggerated tales.

The gameplay for Clank features a blend of stealth and action. He is also featured in a rhythm game for various cinematic spy infiltrations and various driving challenges. Ratchet features his run and gun gameplay in arenas similar to the other games in the series. Qwark has a variety of boss battles and other gameplay challenges that changes as he revises his tall tales.