The USS Vengeance was an alternate reality Federation Dreadnought-class starship under the command of Admiral Alexander Marcus and in the service of Section 31 in 2259. It was constructed at a secret base near Jupiter in the Sol system.
The Vengeance was designed by Khan Noonien Singh for the purpose of preparing the Federation for war against the Klingon Empire, and it was built at a secret spacedock outside Jupiter. When Khan turned on Section 31, he gave Captain James T. Kirk the coordinates for the Vengeance’s location, which were passed to Scotty – who was on leave – to investigate.
Following Kirk’s capture of Khan, the Vengeance rendezvoused with the USS Enterprise in Klingon space. Marcus demanded Kirk hand “Harrison” over, but Kirk refused and had the Enterprise warp to Earth, so Khan could stand trial and expose the admiral’s alliance with the war criminal. The Vengeance was capable of catching up and firing on the Enterprise in subspace, halting its path as it arrived outside Earth. Marcus prepared to finish off the Enterprise, but Scotty, who had stowed away onto the ship, deactivated its weaponry.
Kirk and Khan donned thruster suits and flew over to commandeer the Vengeance. Once they arrived on the bridge, Khan killed Marcus and seized control of the ship for himself. Acting captain Spock transported the 72 photon torpedoes containing Khan’s fellow Augments from the SS Botany Bay in return for Kirk and Scott, as well as the Enterprise’s safety. Khan returned Kirk and Scott, but resumed firing on the ship anyway. Spock had predicted Khan’s betrayal, and having ordered McCoy to remove the cryostasis chambers from the torpedoes, had them detonated in the Vengeance’s cargo bay, crippling the ship.
The Vengeance was caught in Earth’s gravitational pull, and Khan directed the ship to crash at San Francisco in one final act of spite against his former masters. The enormous ship cut through the city, obliterating landmarks like Alcatraz Penitentiary. A year later, Kirk held a memorial for the lives lost because of Khan, including those killed when the ship crashed, and spoke out against what the ship represented, reminding his fellow officers that Starfleet had risked becoming as warlike as their enemies.