after a brief memorial for qwark on the phoenix, ratchet goes to assist ranger forces battling a tyhrranoid invasion in the city of metropolis. unveiling his newly completed biobliterator, nefarious uses it to turn both metropolis's citizens and his tyhrranoid soldiers into robots. making yet another escape, he orders klunk to kill ratchet. after besting the clone, ratchet and clank are reunited and vow to stop nefarious. while searching the remains of the leviathan, they find evidence that qwark faked his death. a secret message hidden on board the phoenix reveals the location of a secret hideout where qwark, overcome with cowardice, refuses to fight any longer. after fighting off an attack on the phoenix, the duo intercept the biobliterator and clank destroys it with an ion cannon. however, sasha informs them that a second, more advanced, biobliterator is being prepped for launch at nefarious's main command center on planet mylon, ratchet and clank locate nefarious and defeat him, but he activates the biobliterator, which transforms into a giant, heavily armed robot. before he can crush the two, a reinvigorated qwark flies in to distract him, giving the duo an opening to destroy the biobliterator. nefarious doesn't bother to specify a destination when he engages his teleporter, stranding him and his butler lawrence on a distant asteroid. with nefarious defeated, the q-force and their allies attend a private screening of the latest "secret agent clank" holofilm.