|“||Dr. Nefarious is aboard a star cruiser called the Leviathan.||”|
The Leviathan was a blue star cruiser owned by Dr. Nefarious, serving as one of his primary bases during his organic life form vendetta campaign in the Solana galaxy and his second base for operations. He commanded much of his army from aboard this ship and abode alongside his servant, Lawrence.
|“||Auto-destruct sequence initiated. Prepare to die.||”|
— The Leviathan's computer upon it's self-destruction activation, UYA
The Leviathan had a great deal of security, with several patrols of Soldier Bots and Ninja Bots. The first hallway contained four Tyhrranoid Dropships. There were also metallic claws hanging from the ceiling that clutched spare components. The second hallway started atop the ledge above the first. Around either corner of the structure here was a small corridor with a bridge above a river of green acid. At the end of this corridor was a platform that rose to another ledge. Up here was a white statue of a Soldier Bot standing at attention. Behind this were small ledges around two short staircases. Before the stairs was a ramp going to the elevator that led up to the ship's command bridge.On the bridge, Dr. Nefarious sat in a control chair that operated the entire ship. Around it were large glass windows that viewed the surrounding space. In front of the doctor's chair stood a holo-screen where he could watch holo-vision programs and presumably see other things around the galaxy. Above Nefarious's chair was a turning mechanism that had two plates circling it and sharp points on the bottom, more red lights surrounding the top dish in the ceiling and silver poles sticking out the dish. On either side of the bridge platform were metal cranks, and two archways above the platform had twelve green-glowing objects with spikes. The front of the bridge had more red lights around it.
Lawrence performed various household tasks for the doctor aboard the ship. After broadcasting his plans to the entire galaxy from his office in his secret base on planet Aquatos, Dr. Nefarious returned to his flagship. On the bridge, he took time off and watched Secret Agent Clank, telling his butler not to disturb his 'work.' Holding a laundry basket, Lawrence came to the bridge and informed his superior of the break-in at his 'impenetrable' Aquatos base and the theft of a data disc. Before Lawrence could leave to continue with "dirty laundry and whatnot," Nefarious demanded to know who was responsible.
The butler informed the doctor that his old nemesis, Captain Qwark, and his newly assembled team, the Q-Force, had been responsible for the infiltration. This greatly outraged Dr. Nefarious, and he ordered Lawrence to have the team annihilated. When Ratchet and Clank traveled to the doctor's base on planet Daxx, where Lawrence and Nefarious had briefly been, they discovered that robotic pop star Courtney Gears was in league with him and that his Biobliterator superweapon had been moved to the Obani Moon System. They first traveled across the moons and discovered that something was going on at Obani Draco.
Unable to get to the last moon, Ratchet and Clank went and met Courtney Gears at Annihilation Nation, hoping to get information on Dr. Nefarious from her. Clank then had her cast as a character on Secret Agent Clank, after which she agreed to provide any desired information. Once Clank approached her about the doctor, she knocked him out and brought him to Nefarious. When Clank refused to join the doctor's cause, he imprisoned him and had his doppelganger, Klunk, replace him at Ratchet's side. The evil twin told Ratchet of the Leviathan, where Nefarious had returned. Ratchet then discovered that Skid McMarx was captured by Courtney Gears on Obani Draco.
Defeating the pop star in her studio, Ratchet found out from Captain Sasha on the Starship Phoenix that the Leviathan had been found refueling at the Zeldrin Starport. Ratchet suspected that it was a trap, Courtney Gears setting them up, but nonetheless took the opportunity to stop the Dr. Nefarious. Ratchet, Klunk and Qwark infiltrated the ship and fought past the security patrols until they arrived at the bridge. Here, Nefarious and Qwark mocked one another, and the doctor revealed that he had indeed trapped them. He wanted to lure them there to witness their demise. He then activated the ship's auto-destruct sequence.
Dr. Nefarious and Lawrence then teleported away, Lawrence at first leaving the doctor behind as a joke. As Ratchet and Klunk hastily went down the elevator, Captain Qwark spotted a valuable data disc and attempted to retrieve it as the rest of the cruiser broke apart. While Klunk forced their shuttle out the docking bay before Qwark could return, the exploding ship fell from orbit and down to the surface of planet Zeldrin. Ratchet and the real Clank later explored the Crash Site of the ship and discovered that Qwark had secretly gotten to an escape pod before the crash, having abandoned the fight against Nefarious for his own safety. They then returned the data disc to the Phoenix, and it proved invaluable in ending the doctor's diabolical schemes.