Khan's Attack and the Fall of the Vengeance

In the Kelvin timeline, Starfleet's Section 31 revived Khan Noonien Singh, a genetically engineered tyrant of the 20th century, and forced him to design weapons under the alias John Harrison. Admiral Alexander Marcus held Khan's crew, still in cryosleep, as leverage. In 2259 Khan struck back, bombing a secret Section 31 facility in London and then attacking an emergency meeting of senior officers at Starfleet Headquarters, where Christopher Pike was killed.

Khan fled to the Klingon homeworld Qo'noS. Marcus sent Kirk and the Enterprise after him with experimental torpedoes, secretly hoping to provoke a war with the Klingons; the torpedoes in fact held Khan's sleeping followers. After an uneasy alliance against Marcus and his dreadnought, the USS Vengeance, Khan seized the warship and crippled the Enterprise.

Kirk gave his life to restore the Enterprise's warp core, and Khan crashed the Vengeance into San Francisco, causing heavy destruction. Spock captured him, and Khan's genetically enhanced blood was used to revive Kirk. Khan was returned to cryosleep, and a year later the Enterprise departed on its five-year mission.