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The USS Vanguard was, according to Khan Noonien Singh, the Kelvin timeline Federation starship in the 2250s decade. Vanguard was one of a select few Section 31 vessels under Admiral Alexander Marcus sent on deep survey missions to catch threats to the Federation. (TOS - Khan comic: "Issue 5")
The SS Botany Bay drifted in space until it was discovered sometime in the 2250s by the USS Vanguard, following the destruction of Vulcan. Admiral Marcus of Section 31 brought Khan out of suspension at the Io Facility, believing his savage intellect would be a prime asset. Khan then underwent facial reconstruction, vocal modulation and had his memory wiped. He forced Khan into working with him by threatening to kill his fellow Augments, and set him to work designing weapons and ships for Starfleet, including the Dreadnought-class USS Vengeance. Khan was recruited under the new identity of Commander John Harrison. Khan, when he first came to, was told by Marcus that he had been on a mission to Qo'noS where he was seriously injured and suffered memory loss. During his "recovery", Khan was given access to his "John Harrison"'s service record by Lieutenant Yuki Sulu. (TOS movie & novelization: Star Trek Into Darkness; TOS - Khan comic: "Issue 4")