After word spreads of Ratchet and Clank's recent conquest in Ratchet & Clank: Going Commando, Clank finds himself recognized as an interstellar robot of mystery and intrigue after starring in his own television series, Secret Agent Clank. While Ratchet is dismayed by his new sidekick status, the feelings are put aside when the twosome is called together by the Galactic President to bring peace to the universe. They find themselves traveling back to Planet Veldin to battle Dr. Nefarious, a robotic supervillain who has devised a diabolical scheme to wipe out all organic life in the galaxy. To reach his goal, he has instructed the Tyhrranoids, a race of multi-eye aliens to annihilate the organics, not knowing that if the Tyhrranoids are successful, they will end up causing their own extinction.