In 2259, Captain James T. Kirk is removed from command of the starship USS Enterprise for violating the Prime Directive after exposing the ship to the primitive inhabitants of the planet Nibiru in order to save them, and Spock, from a cataclysmic volcanic eruption. Admiral Christopher Pike is reinstated as commanding officer with Kirk demoted to first officer. Spock is transferred to another ship. Shortly after, Starfleet officer Thomas Harewood, sent by Commander John Harrison, bombs a Section 31 installation in London. During an emergency meeting on the situation, Harrison uses a ship to ambush and kill Pike and other senior officers, before transporting to Kronos, homeworld of the hostile Klingons. Star Trek Into Darkness 2013
Admiral Alexander Marcus reinstates Kirk and Spock to Enterprise with orders to kill Harrison using a new long range stealth torpedo. Chief Engineer Montgomery Scott objects to allowing untested torpedoes on board without knowing their specifications; when he is overruled, he resigns. Kirk assigns Pavel Chekov to replace Scotty. En route to Kronos, Enterprise‘s warp capabilities become disabled. Kirk leads a team with Spock and Uhura to the planet, where they are ambushed by Klingon patrols. Harrison appears and kills the Klingons. Harrison surrenders when he learns the precise number of torpedoes on board Enterprise.
Dr. Leonard McCoy and Marcus’s daughter, Dr. Carol Marcus, open a torpedo at Harrison’s urging, revealing the torpedoes contain cryonically-frozen humans. Harrison is taken to Enterprise‘s brig, where he reveals his true identity as Khan Noonien Singh, a genetically engineered superhuman, awoken by Admiral Marcus from centuries of sleep and forced to develop advanced weapons. Khan reveals that Marcus sabotaged Enterprise‘s warp drive, intending for the Klingons to destroy the ship after it fired on Kronos, sparking war with the Klingon Empire. Khan also gives Kirk a set of coordinates, which Kirk asks Scott to investigate. Scott discovers the coordinates lead to a covert Starfleet facility.