Khan rules a vast empire, consisting of alternate versions of the planet Earth throughout the myriad dimensions of the multiverse. Using his alien technology, he and his armies can travel from world to world, and for those that to surrender to him, they prosper from the technology he brings, although they live under his iron rule. Those that fight him, have all ended up defeated and subjugated.
During the first assault of Khan on the X-Men's Earth, centered in Madripoor, Storm's splinter group, known as the X-Treme X-Men, were able to capture him. One of Khan's lieutenants, Shaitan, was able to rescue Khan, and in the escape, Khan took with him Storm, who had been injured by Viper. During his captivity, he had become infatuated with her.
Khan continued the invasion, while announcing his intentions to make Storm his queen. Storm refused Khan's advances and managed to escape, although she had to do so while still recuperating and even had to face Khan's harem in battle. When the portal through which the invasion forces had come started to close in on itself, Khan ordered the palace connected above the tower to separate and maintain the portal. The splinter group of X-Men fired at the palace, and it crashed. It is unknown if Khan had survived the explosion that came after.
- In X-Men: The End Vol 3 #2, the Shi'ar empire's new Chancellor is impersonated by Khan. Though in disguise, Gambit finds out his identity.
- 8 Appearances of Khan (Alien) (Earth-616)
- Minor Appearances of Khan (Alien) (Earth-616)
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