Previously in STAR TREK: KHAN... : The Eugenics Wars are over. The augmented humans who rose to power in the 1990s saw their empires crumble as they battled each other for world supremacy. The normal humans they once enslaved rose up to fight back with the help of a bioweapon targeting the Augments' unique physiology. Khan Noonien Singh and his surviving Augment brethren were forced to leave Earth aboard the Botany Bay. Their destination, deep space. Their fate, Unknown, even hundres of years later...
In Section 31's Io Facility, Alexander Marcus oversees the awakening of John Harrison, suffering from heavy amnesia after a failed mission into Klingon territory. After providing a small background, Marcus meets with Yuki Sulu who orders her to let him worry about Khan who is currently researching his fake identity after a flash of his memories.
The next morning, Harrison is showed to his new office, the drydock of the USS Vengeance. Before he returns to work though, Harrison questions the sparseness of his file, noting that it reads as though he had no life outside of Starfleet with Marcus responding that Starfleet was Harrison's life.
Over the next five months, Khan exceeds Section 31's expectations, revamping the warp drive to near Warp 10 speeds, has begun developing a new form of undetectable photon torpedo, and refined the station's computer systems. Though that last piece of information gives Yuki concern, Marcus again waves her worries aside. When Khan remembers who he is, Section 31 will be ready.
After experiencing a flash of Augment soldiers, Harrison reports to Marcus who theorizes that the memory is of the earlier mission to Praxis. Agreeing, Harrison proposes he be sent back there, hoping to now target every mining site and destroy the moon, something he can accomplish via his latest invention: a portable transporter.
With his device successful, Harrison materializes on Praxis. Marcus and Yuki note however that if he faces combat, he will discover his true strength.
On Praxis, Harrison is caught off-guard by another memory before he is surrounded by Klingons. With little effort, he dispatches them before beaming down to Kronos to watch the moon's destruction. As fire consumes it, Harrison's mind flashes back to the last time he saw that much fire, allowing him to remember who he is. Seething with fury, he informs Marcus of his success and begins making his way home.
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Khan, Issue 3
Khan, Issue 5