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In the mid-23rd century, Alexander Marcus used it as headquarters for his operations whilst working with Section 31. He would use it as the setting for the resurrected Augment Khan Noonien Singh who was awakened from the SS Botany Bay by the USS Vanguard, surgically altered and had his memory erased. Marcus would trick Singh into believing he was a Starfleet agent by the name of John Harrison. With his genetically engineered intellect, Admiral Marcus would convince Harrison designing weapons as well as technology that culminated in the Dreadnought class starship known as the USS Vengeance. This was in order to prepare the Federation for an eventual war with the Klingon Empire. It was here that Khan was able to create a personal transporter to carry out the destruction of Praxis. (TOS - Khan comics: "Issue 4", "Issue 5")
By 2259, Harrison had regained his true memory and went rogue where he began staging attacks against Starfleet from Qo'noS. Admiral Alexander Marcus would manage to trick Captain James T. Kirk into hunting the genetic superman whilst the Io Facility continued the completion of the USS Vengeance. Khan would inform Kirk of the coordinates of the station in Io's orbit where he asked Engineer Montgomery Scott to investigate. Mr Scott managed to travel to the facility in a shuttlecraft where he succeeded in infiltrating the large shipyard and boarded the USS Vengeance when Marcus took command of the ship from Io Facility. (TOS - Khan comic: "Issue 5"; TOS movie: Star Trek Into Darkness)