In high school, Nefarious had been constantly bullied and humiliated at the hands of Captain Copernicus Qwark, who was 26 years old and three times Nefarious' size at the time. He then became a mad scientist trying to take over the galaxy. Later, Nefarious launched an amoeboid invasion on Blackwater City. Qwark confronted Nefarious on a catwalk overlooking churning gears and machinery. After recognizing him from high school, Qwark threw him off the catwalk , into the spinning gears below. Qwark thought that he had destroyed Nefarious but he survived, although he was forced into being a robot because his body was beyond repair. He since aquired a vicious hate for all organic life and made it his mission to destroy all "squishies" in the galaxy.
Attack on Metropolis
Some time later, Dr. Nefarious attacked Metropolis with a massive horde of Robotic Bugs that consumed various forms of matter. However, Qwark once again defeated him. But Nefarious captured Qwark after Nefarious' butler Lawrence saved him, and they imprisoned him in a secret facility. Qwark managed to escape to his hideout on the Thrann Asteroid, where he hid until Nefarious allegedly disappeared. He was secretly making plans for his next attack.
The Bio-Bliterator Scheme
Dr. Nefarious is a mad robotic scientist and main villain in Ratchet and Clank: Up Your Arsenal. He planned to turn all life into robots with his superweapon, the Bio-Bliterator. Throughout the game he is assisted by his English robotic butler, Lawrence. Through their arguments we learn that Nefarious once tried out in Galactic Idol, singing 'Crushing on Squishies', failing horribly in the process. The tape from his performance is said to be used in prisons for torture. He ultimately failed as he was defeated by Ratchet and Qwark. He, as a last resort teleported himself to a random coordinate. He ended up on a deserted asteroid extremely far from any civilization.
Often, while under great stress or pressure, Nefarious will lock up, resulting in the audio from various soap operas being played instead. Lawrence is required to smash him on the back of his head allowing him to return to his original state. He and Lawrence also make a brief cameo appearance in Ratchet: Deadlocked, where they are seen gradually approaching Gleeman Vox's DreadZone Station, only to watch it explode right in front of their eyes.
He appears as a floating image in Ratchet's Dreamtime level in Ratchet and Clank: Size Matters, along with other characters such as Chairman Drek and The Plumber. Although he doesn't feature on screen in Ratchet and Clank Future: Tools of Destruction, Captain Qwark announces over the PA system in Mukrow Arena, 'Would a Dr. Nefarious please report to the office, we have recovered your wallet'.
Great Clock Scheme
One day, the Fongoids saved Nefarious and Lawrence after they landed on planet Zanifar, but still Nefarious could not get over being defeated again. Thus he had to go through many steps to redeem himself, until finally he discovered the Great Clock. With the clock under his control, he went on about, he would be able to wrong all the rights in the universe, in which the heroes always lose and the villains always win. He became allies with Pollyx and Flint Vorselon to create the Nefarious Space Station. He told the Zoni to bring Clank to the Great Clock to continue his plan. His use of the Hyper Sonic Brainwave Scrambler made the Zoni scatter and leave the Clock.
Ratchet & Clank: Up Your Arsenal
In Up Your Arsenal, it was revealed that he and Qwark, who was 26 years old at the time, attended high school together. Qwark would often bully Nefarious, who attempted to get his own back, but eventually was badly injured, resulting in him becoming a Cyborg. As a result of these humiliating times, Nefarious built up a strong hatred to all natural creatures, harboring plans to eliminate all non-robots from the galaxy.
He built a powerful weapon called the Bio-Bliterator, capable of turning all organic life into robots. To help him carry out the war, he recruits an army of Tyhrranoids, well trained but stupid enough to not realize they were under threat as well. Realizing the Q-Force may be try to prevent his plans from coming to fruition, Nefarious hires Courtney Gears to work for him. After Ratchet won in the Annihilation Nation, she knocks out Clank bringing him to Nefarious. He then offers Clank the opportunity to rule the galaxy with him, though he refuses and manages to escape. Gears, who seems to be romantically interested in Nefarious, also kidnaps Skidd McMarxx, allowing them to test the Bio-Bliterator on him.
Allowing Big Al to track down a transmission, Nefarious sets up a trap, rigging the Starship Levithian with explosives. Ratchet and Clank manage to escape and find him just about to launch the Bio-Bliterator, resulting in a final battle. At the end of the fight, the Bio-Bliterator is put on self-destruct, but Nefarious and Lawrence manage to teleport to a nearby asteroid, escaping death. While there, Lawrence reveals that they are unlikely to come across any planets for anywhere between 5 and 10,000 years, causing him to lock up.
Ratchet & Clank Future: Quest For Booty
In the epilogue of Ratchet and Clank Future: Quest For Booty, Dr. Nefarious makes a brief, yet comical entrance - falling over Lawrence's duster. It is revealed that the Zoni have requested his assistance in fixing the now malfunctioning Clank, though its not known whether they are in alliance with him.
Ratchet & Clank Future: A Crack in Time
Nefarious returns as the primary villain in Ratchet & Clank Future: A Crack in Time. Initially, he is employed by the Zoni to help them fix Clank. After being not able to go into the Orvus Chamber by the Zoni, however, he ends his partnership with them and activates the Hypersonic Brainwave Scrambler and sends it to chase the Zoni out of the Great Clock. This caused an attck in the clock and all the Zoni to run away, as well as giving Nefarious' troopers malfunctions.
Nefarious and Lawrence can be seen on the screens throughout the Great Clock as Clank escapes with the help of Sigmund, but Nefarious soon finds Clank and tells him where he is and revealed it to be his home, the Great Clock, built by the smartest Zoni in the universe and constructed in the center of the universe (give or take 50 feet). Clank then asked the doctor what lie he told the Zoni in his quest for vengeance, and Nefarious sarcastically replies "You think I went though all this trouble for mere vengeance? Well, lets just say its all in the past." And then calls his robotic butler by his name, Lawrence, and tells him to "ready the orb of mobilization" which knocks Clank out.
Lawrence then asks Nefarious if he should repair the station Clank was being held in again, but the doctor had a better idea in mind, and told Lawrence to just wait, as they don't need to worry, they have all the time in the universe. He is later seen trying seen making his own play, which he calls "Night of the living Squishes", where he is then interupted by Lawrence, who says he thought it would be important to tell him that Clank is heading to the Orvus Chamber, and that his plan his working, but there is one small matter.
Lawrence shows the doctor of a picture of Ratchet and Qwark, who are looking for Clank and trying to stop his evil plan, causing him to shout "Qwark!" and freeze up, but was smacked to snap him out of it by one of his troopers. And then tells his butler that they cannot be able to meddle in their plans, and his troops need to track them down and destroy them. Lawrence confirms he will do that right away, but in the mean time Nefarious should turn on the safety in his gun, so he can't accidentally kill anymore troops. Nefarious shoots the gun and tells him its armed, but he was wrong and the blast went and killed another one of his troops. Nefarious, upset, then ordered another troop to be Qwark for his play.
After breaking into Pollyx Industries, Ratchet and his new Lombax friend see the doctor on a screen as he sarcastically said greetings to his old enemy and that it's been a long time since we've seen each other and that he's sure he thrilled to witness his greatest plan. Nefarious then noticed that Ratchet met Azimuth, and its a pity the first Lombax he met is the shame of his entire race, apparently knowing of Alister's past
Ratchet then sarcastically asked what he was up to this time, if he was trying to turn the universe into robots again or if it was just good old galactic domination. Nefarious replied by saying he wanted to let Ratchet live long enough to find out but the other part really just wanted to kill him for old times sake. Nefarious then activated the VX-99 machine to destroy Ratchet and Alister and the city along with them to get them. After destroying the bottom and arms of the machine, Ratchet fought the main power, which was controlled by Lord Vorselon, Nefarious' new partner, but it was soon defeated and destroyed by him, activating its self-destruct, which Ratchet escaped. Lord Vorselon then returned to the Nefarious Space Sation and informed the doctor that Ratchet and the elder had defeated the VX-99 and escaped.
Nefarious, mad at his defeats, screamed "unacceptable" and that he "practically handed those squishes to him on a silver platter" and threw a globe from his desk at him but he warped out of the way and hid behind Lawrence before he left to leave them alone. Nefarious then once again informed Vorselon that if Ratchet, Alister, or even Qwark find the clock their plans would be ruined and his body will remain crushed and abandoned on planet Zaurik, where Vorselon had a war with the Drophyds. Nefarious then sarcastically asked Vorselon if that's what he wants to happen instead of getting his body back, and Vorselon shook his head while making a sad puppy dog face, and Nefarious brought in specialist, Cassiopeia, Carina and Libra, and agreed that if they helped him he would bring back their colony that was destroyed in a supernova, and so the Valkyries agreed.
After sending Libra to kill Ratchet, Nefarious also began to grow a relationship with Cassiopeia, who was found seducing him at times. After discovering Orvus, Clank's father and leader of the Zoni, was last seen with Nefarious on planet Zanifar, Ratchet was sent by Clank to find and save him by traveling in a time portal to years into the past. After breaking into his lab on the planet, Ratchet saw Orvus who was being contained in a glass dome by Nefarious, was being tortured by the Hypersonic Brainwave Scrambler controlled by the doctor who attempted to do this thinking he would give up the Great Clock's location.
After trying many times, Nefarious gave Orvus one last chance to tell him how to get into the Orvus Chamber but Orvus still refused to tell him, and with Nefarious losing his temper, he ordered the Hypersonic Brainwave Scrambler yo be put on full blast. Orvus, despite him being incredibly weak, still would not tell him, and as everyone in the room feared the blast would create an explosion, said that there is only one in the universe that could enter it and he is safe far from you, and cut off the blast and disappeared. Nefarious could not tell what happened to him, and asked Pollyx where he went, but Pollyx also had no idea and put up a image of him before he dissipated which showed Clank. Ratchet, puzzled that a picture of Clank would come up said, "Clank?", causing Nefarious to hear Ratchet. But before Nefarious stopped Ratchet, he threw one of his bombs at Nefarious' face creating a scar and giving him a broken eye. Nefarious, furious but puzzled that Ratchet would be there said, "destroy him. you fools" to his troopers while Ratchet got away.
In the present time, Nefarious and Cassy were sitting on the chair together, with him apparently telling her of what happened when he kidnapped Clank, but just as Cassy, who was seducing him often, was about to say he's so, so presumably handsome, he was cut off. Then the Ratchet throwing his bomb at Nefarious' face begin to effect in the president, and Nefarious, who started to remember what happened said, "Ratchet!"
Nefarious and Lord Vorselon were later seen playing video games together, with Vorselon playing as Captain Qwark, and Nefarious playing as himself, however, Vorselon didn't have a body, so it was extremely hard for him to move the controller, and as a result, the Terraklon lost, and Nefarious shouted, "Victory, in your face" at him, whereas Vorselon makes a pouty face. Lawrence then appears as a hologram to tell the doctor that his plan worked and the Orvus Chamber was now under their control. Nefarious jumped up saying, "Splendid", and told Lawrence to tell the Valkyries. He then activated his plan and the Valkyries kidnapped Clank.
However when Nefarious opened the door, it revealed Qwark, who was in a nurse outfit. Nefarious knew it was him, but played along. Nefarious is heard on Vapedia talking to Cassiopeia, who was constantly failing to kill Ratchet. She was destroyed after Ratchet fought her in her aircraft. This made Nefarious even more angry, and causing him to betray the Valkyries, as he no longer needed their help without Cassy.
Ratchet, Clank, and Qwark went to the Nefarious Space Station and used a Holo-guise to make a suit for Ratchet. As Ratchet made it to the main control room, where he would kill Pollyx, he destroyed Nefraious' fleet, leaving only one. But, after they succeeded, they were surprised to Nefarious with two guards confronting them. Ratchet, although he knew Nefarious wouldn't give in, kept explaining that "nothing he would want is worth risking the universe" However, Nefarious explained there was, and also explained how he got off the asteroid he was trapped on.
One day, the Fongoids saved them after they landed on planet Zanifar, but still Nefarious could not get over being defeated again. Thus he had to go through many steps to redeem himself, until finally he discovered the Great Clock. With the clock under his control, he went on about, he would be able to wrong all the rights in the universe, in which the heroes always lose and the villains always win. Nefarious laughed and strapped Ratchet & Clank to an asteroid, and trapped Qwark. Ratchet continued to tell Nefarious he was making a mistake even he would regret, but Neffy said "time will tell" and said goodbye to his old "friends." But suddenly froze from being over excited, however he was still able to launch Ratchet & Clank into space. He presumed they were dead after this and called Lawrence to pick him up with the last saucer
Qwark escaped with his pet Snowball's help, and Ratchet & Clank were saved by the Zoni. Both heroes managed to use a ship to make it back to the station after landing on another planet. Ratchet & Clank then confronted Nefarious, who was surprised to see they survived. Clank told him to shut down the transport saucer and stop his madness, but Nefarious mockingly said "Look at you! Free for the first time in years, inches from your destiny, and what do you do? Run right back to playing backpack to a squish! Your nothing but a sidekick" Lawrence sarcastically said to Clank "We should hang out some time" knowing he was also a sidekick.
Ratchet was furiously upset by Nefarious' comment about Clank saying "No one talks to Clank that way!" Ratchet then said he would let Clank choose to go with him, or stay at the clock after they kicked Nefarious' butt and defeat him. Nefarious activated his rocket boots and said "When I'm finished killing you, I think I'll rewind time, so I can do it again, and Again, and AGAIN!!! hahahahahah!" and said he's been waiting a long time for this. He then started his long and extremely epic battle with Ratchet & Clank, saying "You'll pay for what you did to my eye" The heroes managed to put damage on him, but he then activated the Hypernove Defence Laser and sent it to kill Ratchet and Clank, saying to them "Didn't see that coming, did ya?"
The heroes soon got to his flying saucer, where Nefarios ordered Lawrence to do something, as he was seemingly running out of ideas to stop them. They continued to fight on the saucer as it was heading for the Great Clock, however, the auto-pilot malfunctioned, causing trouble for the heroes. Ratchet and Clank managed to damage Nefarious to the point where his rocket boots would cut out, and he would malfunction. Nefarious soon fell to his saucer, malfunctioning, as the auto-pilot headed straight for the Nefarious Space Station. Ratchet urged Nefarious to tell him how to deactivate the auto-pilot, but the doctor would not respond. Lawrence then took and escape pod making matters worse, and leaving Ratchet and Clank to die on the saucer. However, Alister Azimuth appeared to save Ratchet & Clank, as they jumped into his ship. Unbeknownst to anyone at the moment, Lawrence teleported Nefarious' body away. The saucer finally crashed into the station, forming a scar just like Nefarious, and destroying it.
During the games credits; new reporters Kip Darling and Pepper Fairbanks reported Nefarious' remains weren't found in the destroyed station nor were Lawrence's, and Galactic authorities were mobilized to find them.