USS Enterprise (NCC-1701 alternate reality)/Service history/John Harrison

That evening, the rogue agent John Harrison attacked Starfleet Headquarters to assassinate Marcus, but killed Pike instead. Marcus gave a vengeful Kirk permission to take the Enterprise to Qo'noS where Harrison had fled, and fire on his location with 72 advanced long-range torpedoes. Chief Engineer Scott protested the loading of the photon torpedoes aboard Enterprise without his chance to examine them, offering his resignation, which Kirk accepted. Chekov was appointed as Scott's replacement.
Kirk found Harrison on Qo'noS and had him brought to the brig. Harrison was reticent about his motives, but suggested Kirk examine the torpedoes Marcus gave him, and also gave him a set of coordinates, which the captain sent to Scott to investigate. 
Marcus's daughter and McCoy opened up a torpedo and discovered it held a man in cryogenic stasis. Harrison revealed he was and the torpedoes held his fellow Augments, with whom Marcus had threatened him into cooperation. Marcus arrived in the and demanded Kirk hand over Khan, but Kirk refused, intending to expose the conspiracy by bringing Khan to trial on Earth.
The Vengeance caught up with the Enterprise at warp and fired on it, halting it as it arrived just outside Earth. Marcus beamed up his daughter before preparing to wipe out all other witnesses to his plot, but Scott, who had sneaked aboard the Vengeance at the coordinates given by Khan, temporarily deactivated its weapons. Kirk and Khan donned thruster suits to commandeer the Vengeance, while Spock ordered McCoy to remove the cryo tubes from the torpedoes.
Aboard the Vengeance, Khan killed Admiral Marcus and demanded Spock hand over the torpedoes in exchange for Kirk, Scott, and Carol and the safety of the Enterprise. Spock, knowing Khan would renege on letting the Enterprise survive, set the transported torpedoes to detonate in the Vengeances cargo bay. The damage inflicted caused both ships to hurtle to Earth: the Vengeances engines were compromised while the Enterprise's warp core became misaligned, causing loss of power and propulsion. As the ship plummeted toward Earth, Kirk realigned the ship’s warp core despite Scott’s warning about the high radiation levels.