Ratchet and Clank were enjoying a break from their adventures at Ratchet's garage on Veldin when a beautiful star yacht came to his garage for repairs. At the same time, Dr. Nefarious's planned to defeat Ratchet once and for all with some help.

Ratchet and Clank are cleaning up a Amoeboid miss caused by Dr. Nefarious. They have one more batch of Amoeboids to take out in Metropolis. For this last mission, they are joined by a hero-in-training from Sailor Moon's dimension, Genji Kazemaru.