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This page details Khan Noonien Singh in alternate universes; for Khan Noonien Singh in the primary universe see Khan Noonien Singh; for the Khan Noonien Singh in the mirror universe see Khan Noonien Singh (mirror); for Khan Noonien Singh in the alternate reality created by Nero's temporal incursion see Khan Noonien Singh (alternate reality).

In an alternate timeline in which the Augments won the Eugenics Wars, Khan became the ruler of a genetically engineered Human race called the Children of Khan who sought to conquer all of known space. His followers managed to conquer the planet and Khan himself was noted to have finished his conquest of the United States by arriving in Washington, DC in order to accept the President's surrender. His actions led to the Great Ascension of Humanity and he led his people as the First Khan, the Eternal Master and the First Lord of Mankind. Through his actions, he managed to lead his people against numerous alien races and conquered them such as the Andorians, who knelt in servitude before him.

His empire, the Khanate of Earth, later came under attack from the Romulan Star Empire during the Earth-Romulan War. At some point, he was noted as having seduced and killed a Romulan commander after which he stole a cloaking device from the Star Empire. It was noted that he died as an elderly statesman after living for over two centuries and had a grandchild who continued to lead the Augment empire. Through his leadership, he became a well-respected leader of his people and revered by them for centuries.

Before his death in 2172 at the age of 213, he was also involved in a program that led to his intelligence and memories being implanted into a computer. With the development of holotechnology, this intelligence was capable of manifesting the appearance of Singh in various points of his life. The program was highly sophisticated as it required three times the processing power of a normal holoprogram. This created a potent counsel which only high-ranking Princeps were capable of accessing and thus gained a measure of Khan's wisdom as he advised these younger Augments on their role in the future of their race.

By 2376, his grandson Tiberius Sejanus Singh reigned as the Khan Imperator of the Khanate of Earth. (DS9 - Myriad Universes novel: Seeds of Dissent)

In another alternate timeline, USA Today reported that US President Bill Clinton had surrendered the United States of America to Khan. (Last Unicorn RPG module: All Our Yesterdays: The Time Travel Sourcebook)

Benjamin Sisko was once timeshifted to an alternate reality in which he watched Khan declare victory on 27 October 1995. (DS9 comic: "No Time Like the Present")

In a timeline in which the Xindi had destroyed Earth in 2154 and the Human colony on Ceti Alpha V in 2165, the SS Botany Bay was discovered and its passengers revived. Dismayed and enraged at what they found, Khan and his followers became the leaders of the few remaining humans, rallying and inspiring them to strike back against the Xindi. Khan personally forged an alliance with the Klingon Empire, bringing them and other races to his cause. After defeating the Xindi, humanity began to rebuild their civilization and seek out their enemies. (ST short story: "Dawn")