From wikipedia:
"The story of the game continues from where Quest for Booty left off, and will follow Ratchet continuing his search for Clank, who was kidnapped by the mysterious Zoni at the end of Tools of Destruction. Ratchet discovers that Clank's kidnapping was engineered by Doctor Nefarious, the main antagonist of Up Your Arsenal, and sets out to rescue him.[6] It is hinted at in the second trailer that Dr. Nefarious might be trying to control time. [7] Also, in Tools of Destruction, Clank says that the Zoni can travel though time, which might suggest that they are being used by or are in league with Dr. Nefarious. Another Lombax also plays a large part in the plot, named Alister Azimuth"

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