Dr. Nefarious

Dr. Nefarious was a robotic mad scientist who hated organic life forms, despite formerly being one himself. He was also the archenemy of renowned intergalactic 'superhero', Captain Qwark, and later a recurring adversary of Ratchet and Clank. Nefarious was the main antagonist in Up Your Arsenal. Potting to turn all organisms into robots, and was defeated, but survived. He made several cameos in further games, recurring more than any villain, and returned as

Arsenal
Dr. Nefarious is the main boss in UYA.

Biobliterator Threat
Ten years later, Dr. Nefarious started an entire public campaign to rid the Solana Galaxy of organic life forms. Nefarious formed an alliance with the Tyhrranoid race,

who served the doctor as his personal army, gullible and oblivious to the fact that they were organic life forms. The heroic duo, Ratchet and Clank, saw a news report detailing an attack on planet Veldin, Ratchet's foster home, by Tyhrranoid soldiers. Dr. Nefarious was believed to be the attack's mastermind. Later, on the Starship Phoenix, that fact was confirmed when Captain Sasha Phyronix, Ratchet and Clank received a message from him on the ship's bridge, where he announced his plot. Nefarious then launched an attack on the Capital City of Marcadia, which Ratchet and Clank managed to stop. Later on, Clank explored Nefarious' Office in his "impenetrable" secret base on Aquatos, and found out that he was a huge fan of the Secret Agent Clank series. Lawrence informed Nefarious of the break-in on his ship, the Leviathan, while he was watching Secret Agent Clank. This outraged the doctor, and caused him to crash again. After being smacked back to normal, he ordered Qwark's Q-Force, which Ratchet and Clank was a part of, annihilated.

After giving a message to the q-force Dr. Nefarious and Lawrence were then seen on planet Daxx on Supervillian Weekly, being interviewed about Nefarious' new top secret superweapon. Ratchet and Clank explored Daxx, though Nefarious had removed all data on the mysterious device. It was revealed, however, that robotic pop star, Courtney Gears, was in league with the doctor. While on Holostar Studios, Clank needed to film a Secret Agent Clank scenario, with Gears as a character. He asked her what Nefarious was planning, and she was able to capture Clank by knocking him out. She then contacted Nefarious, who was greatly annoyed by her calling him "snooky wookums" (showing that she devoted to the doctors plan of robot freedom), and told her to bring him 'Agent' Clank. Nefarious then tried to turn Clank over to his side, as he was a fanatic of the Secret Agent Clank series and believed them to be real, following his missions from the beginning. He even rejected Clank's assurance that the series was just an act, calling the statement "Lies! Squishy LIES!". His anger caused him to freeze and pick up soap opera signals again. Courtney had to smack him to get him back to normal. When Clank refused to join, Nefarious decided to replace Clank with a doppelganger, kLuNk.

Klunk, posing as Clank, told Ratchet that Nefarious was aboard the Leviathan. Later on, Nefarious launched an attack on Blackwater City which was also stopped by Ratchet. At the Zeldrin Starport, Ratchet, Klunk and Qwark found Nefarious on his ship. Commenting that Qwark had gained weight and going into yet another crashing sequence, Nefarious activated a self-destruct for the ship and commanded Lawrence to teleport them away. Lawrence left himself, leaving Nefarious, who was not amused by the joke, and was then teleported out the next moment. They had to run to their ship before the spaceship blew up. However, Qwark seemed to not make it out. Back in Metropolis, Nefarious showed Clank Klunk's transmission of Ratchet's actions, meaning he could track the Lombax, and claiming that Ratchet would be killed with Clank having a "front row seat". Nefarious then revealed his superweapon, the Bio-Bliterator, which could transform the whole city into robots. He demonstrated by turning his remaining Tyhrannoid soldiers into robots. At first, however, Nefarious accidentally turned on a video recording of his Galactic Hero audition, angering him, as his butler had not set the switch properly.

Ratchet soon found out that the robot on his back was Klunk and Clank had been captured by Nefarious. The doctor mocked Ratchet before leaving with Lawrence, laughing so hard that his sides ached. Ratchet fought Giant Klunk on the Hover Train they were on and managed to defeat him and save Clank. Nefarious then launched another Tyhrranoid attack on Aridia, which was again stopped by Ratchet and Clank. On Koros, Clank used the Nefarious BFG ion cannon to destroy the Biobliterator while Nefarious was screaming furiously from a video screen. Then Nefarious decided to use his second Biobliterator, more powerful than the first, and fueled it on Mylon, but Ratchet and Clank were able to defeat the last of Nefarious' forces and bested the doctor in combat, despite his surprising powers. He called Lawrence to his aid, and ordered his butler to begin the "transformation". The second Biobliterator changed into a pilotable mechanoid. Laughing maniacally, Dr. Nefarious prepared to use his monstrosity to bring about the Age of Robots. However, he was fired upon by Captain Qwark, who arrived on the scene in his own shuttle. He had survived and decided to come out of hiding to help defeat his nemesis. Distraught at this, Nefarious said "No! I don't believe it!", and Qwark said "Believe it, toaster head!"

Ratchet and Qwark defeated Nefarious in the air, and destroyed the Biobliterator mechanoid. The head of the machine landed on the ground of the battlefield, and Nefarious was greatly humiliated by being defeated at the hands of "squishies", believing he would never live it down. The cockpit's computer then announced that the self-destruct system would activate in sixty seconds. Nefarious bluntly told Lawrence to engage the teleporter. Lawrence asked him to specify a destination, and Nefarious just said "Who cares? Just get us out of here." The computer then said time was up, and Nefarious shouted "What!? That wasn't even close to sixty seconds!!" The Biobliterator's head then exploded, and in a panic, Lawrence teleported them far away, to an asteroid in space.