Eugenics Wars
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The Eugenics Wars are a backstory event in the Star Trek fictional universe. First mentioned in the TOS episode "Space Seed", in which it was stated that the Eugenics War was a global conflict that occurred during the mid to late 1990s. The progeny of a genetic engineering project established themselves as supermen and attempted world domination. The most notable of them, Khan Noonien Singh, conquered a quarter of the planet, mostly Asia. They ended up fighting amongst themselves and were eventually overthrown due to their disunity. Khan, however, escaped into space with a group of his followers only to be encountered by the USS Enterprise after spending centuries in suspended animation. Much like the Butlerian Jihad in the Dune universe, the Eugenics Wars are the primary reason for many restrictions and prohibitions on genetic manipulation within the Star Trek universe.
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What is known
At the time "Space Seed" was written, the Eugenics Wars were inferred to be large-scale global conflicts. However, after the very different reality of the actual 1990s, the Eugenics Wars have been retconned in some non-canon Star Trek novels that describe them as much quieter conflicts, secret wars that occurred mostly in the shadows of the major conflicts and events of that decade with Gary Seven and his assistant being Khan's principal opponents. However, the Star Trek: Enterprise episode "Borderland" reaffirmed in canon that 30 million people died in the conflict. In the two-part Star Trek: Voyager episode "Future's End", the crew of USS Voyager was transported to Earth in 1996, where it is shown that, at the very least, the Los Angeles region was spared any direct impact of the Eugenics Wars.
In "Space Seed" Mr. Spock refers to the Eugenics Wars being Earth's third world war. This statement has been quietly ignored, however, and in the Star Trek Universe, World War III is said to have taken place in the mid 21st century, ending in 2053. The use of a plural to describe "Eugenics Wars" has never been officially explained either, suggesting that there was likely more than one conflict within a short period of time (similar to the real world enduring two Gulf Wars in a little over a decade).
The only other mention of the Eugenics Wars in the original series is in the episode "The Savage Curtain," in which Colonel Green is established as a key player in the wars.
Captain Jonathan Archer's great-grandfather was in North Africa during the Eugenics Wars. His battalion was evacuating civilians from a war zone when they came under attack. There was a school full of children directly between them and the enemy. If his men had returned fire, they might have hit it. So he called the commander on the other side and got him to agree to hold his fire long enough to evacuate the school.
An episode of Star Trek: Deep Space Nine ("Dr. Bashir, I Presume") suggested that the Eugenics Wars occurred not in the 1990s, but in the late 21st Century. This was later dismissed as a continuity error on the behalf of the episode writers and not an official retconning of the event.
Enterprise Trilogy
A three-episode story arc of Star Trek: Enterprise in October and November 2004 examines some of the aftermath of the Eugenics Wars in the years before "Space Seed". At least one media report released prior to the broadcast of the arc's first episode, "Borderland", erroneously stated that the series was going to retcon the Eugenics Wars into happening in the 22nd Century, but this turned out to be a false report.
Unofficial Backstory
In 2001 a book by Greg Cox was released that detailed that events of the Eugenics Wars. In the book, the Eugenics Wars were shadowy conflicts fought behind the scenes of current events, against elusive and conspiratorial enemies whose genetically engineered origins remained largely unknown to the general public. Most people were not even aware of the global struggle against Khan and his fellow supermen, seeing only scattered brush fire wars and random acts of terrorism.
Chrysalis
According to the book, genetic engineering in the 1960s led to the Chrysalis Project, an ambitious eugenics program conducted by a group of scientists trying to create a new, artificially improved breed of men and women: smarter, faster, stronger than ordinary human beings, a super-race to take command of the entire planet.
Designed and facilitated by a group of world-renowned geneticists, the top-secret Chrysalis Project involved manipulating chromosomes of human embryos using techniques that appeared to be far beyond what humans were capable of at the time. Essentially its goal was to improve the human race artificially by editing out "bad" influences in genetic structures and adding in "improvements" which would maximize the potential mental and physical development of the subject embryos, which would create a race of superhumans. The designers focused on increasing intelligence, strength, endurance, respiratory capacity and the cardiovascular system. The Chrysalis Project endeavored to give their genetically enhanced creations full rein of the planet. To do so, the engineers of this project also genetically enhanced the bacteria streptococcus, making it a volatile flesh eating entity. In order to infect the worlds populous, Russian ICBMs were procured as implementation vehicles.
Free from any governments authority, Chrysalis was a private consortium that answered to no one, having complete autonomy. Chrysalis had its headquarters located in the Thar Desert, thanks to its remote location, the Chrysalis endeavor was completely isolated. The main complex was hidden beneath the ruins of an ancient Rajput fort.
The Augments
The genetically engineered "Augments" of the Chrysalis Project were mentally and physically superior to ordinary men and women. They were five times stronger than the average person, their lung efficiency was 50 percent better than normal, and their intelligence was double that of normal humans.
The problem was that as one of the Chrysalis scientist wrote before he was murdered by an Augment, "Superior ability creates superior ambition": the so called supermen felt that their superior physical and intellectual abilities gave them the right to rule over the rest of humanity. To that end, they conspired throughout the 1980s to seize power through the use of behind-the-scenes manipulation, brute force and "puppet leaders" who answered only to them.
Khan Noonien Singh
Of all the genetically enhanced manipulators who rose to power during this period, none were as ambitious or as ruthless as the man known as Khan Noonien Singh. The son of the original director of Chrysalis, Dr. Sarina Kaur, Khan Singh's presence was felt throughout the world, perhaps most discreetly. He fought against Soviet soldiers outside Lenin's tomb, where he stopped a coup, and maintained the safety of President Mikhail Gorbachev while he was attending the summit in Reykjavik, Iceland. He was rumored to be all over the Asian and Indian subcontinent, inciting the 1987 pro-democracy uprising in South Korea, fighting alongside the Afghan rebels in their guerilla war against the Soviet Union, personally arranging the 1988 plane crash that killed General Muhammad Zia-ul-Haq, leader of the Pakistan's military government, returning democracy to India's nearest neighbor and rival. Khan was also credited with the so called "natural" death of the Ayatollah Khomeini.
Aided and abetted by power-hungry individuals in various governments, business organizations, and independent agencies who allowed themselves to fall under his domination, Khan attempted to gain control of the entire planet. In 1992 Khan quietly seized power over much of Southeast Asia and the Middle East through blackmail and strong-arm tactics. Dozens of "figurehead rulers" either answered to Khan or in some fashion allied themselves with him.
He ruled his dominion from what he called the Great Khanate in the remote parts of India. His fellow "supermen" took over key positions of power in South America, Somalia, the former Yugoslavia, remote parts of the South Pacific and in sections of North Africa. Khan's Great Khanate was centered in Chandigarh, India and had a secondary command center on Muroroa Atoll, "Chrysalis Island", of the Tuamoto islands in the French Polynesia. On June 14, 1992 from Muroroa Atoll, a former French nuclear testing area (Centre d'Experimentation du Pacifique), Khan launched the Morning Star satellite into orbit, giving him the ability to damage the Earth's ozone layer. On July 10, 1992 Singh held an assembly with delegates from nations in Southern Asia and the Middle East, where he demonstrated Morning Star's abilities and issued an ultimatum, "if I fall, the world falls with me". The satellite would later cause an increase in the hole in the ozone layer that was publicly blamed on the eruption of Mount Pinatubo in the Philippines.
Various incidents of violence around the world were spurred by Khan and his fellow Augments throughout 1992, such as civil wars in Liberia, Peru, Afghanistan, Bosnia, Somalia, Sudan and elsewhere; race riots in Los Angeles and food riots in Albania.
On June 14, 1993 Khan held a summit with 6 of his most powerful Chrysalis siblings, where he attempted to unify them to create a new world order with him as the prevailing voice. The summit was a failure as Khan's dream of unity collapsed when the Augments' enhanced ambition caused them to turn on one another, spawing the Eugenics Wars.
The War
Carried out through mostly covert operations, the war did result in massive casualities that the legitimate governments publicly said were rogue terrorist incidents or natural disasters.
During this time, in their eagerness to assert their self-proclaimed destinies as rulers of the Earth, the Augments sparked civil wars and unrest all over the globe, in Eastern Europe, Liberia, Somalia, Peru, Haiti, Rwanda and elsewhere. Though the public-at-large was aware of the majority of such events - most never knew that the events were in fact all related to one another. Indeed, the public was kept entirely ignorant of many of the related "battles" of the Eugenics Wars and even Khan himself was not known to the majority of the world.
One notably incident of the war occurred on September 30, 1993, when Khan was lured to the Ajorra caves in central India by Vasily Hunyadi, the Augment force behind the Serbian government, who attempted to assassinate Khan by triggering an earthquake caused by an underwater concussive charge place by Hunyadi. This earthquake was in the previously-considered aseismatic region of Maharashtra. The death toll from this quake was over 10,000 and entire villages were destroyed.
Khan attempted to retaliate on February 7 of 1994 during a submarine battle under the Mediterranean Sea between Khan's forces and Hunyadi's. However, his effort was thwarted when the ballistic missile submarine S.G.K. Kaur was attacked because of the no-fly zone imposed by NATO.
A couple of months later, on April 21 Dr. Donald Williams of the Chrysalis Project gave to Khan the genetic sequence for the flesh eating strain of streptococcus-A developed by Sarina Kaur. Khan would begin human testing of this carnivorous bacteria on October 2 of that year.
On August 29, 1994 Hunyadi addressed the United Nations in defiance against the economic sanctions and the NATO peacekeeping presence to declare that Serbia had nothing to apologize for. During his speech, members of the Army of Eternal Vigilance (AEV) released sarin gas, a nerve toxin, into the council chambers, suffocating to death many ambassadors and tourists and also Vasily Hunyadi.
The AEV was an antigovernment militia based in Cochise County, Arizona. It was commanded by an Augment named Hawkeye Morrison. Morrison had teamed up with Khan to eliminate Hunyadi. Morrison's ambition with nerve gas was notorious, the AEV attempted to release Sarin gas at both ends of the Eurotunnel at its opening to the public. When this strike was stopped paranoia consumed Morrison. He attempted to kill all his followers but they escaped and Morrison committed suicide.
On March 17 of 1995 Khan acquired over 200 bio-warheads from the former Soviet Union. Eventually, after learning the secrets of the Chrysalis Project, Khan redeveloped the flesh eating streptococcus that his mother developed and prepared to devastate the planet with its presence. On September 5, 1995 Chrysalis Island was attacked by a joint Russian-American strike, a ten-kiloton nuclear device destroying Khan's biological warfare lab and his doomsday weapon. The cover story was that France had privately resumed nuclear testing in the area of the old Centre d'Experimentation du Pacifique.
With his weakened arsenal and with the major superpowers of the world now aware of Khan's plans of genocide, air strikes from American B-52 bombers and a ground assualt from the Russian Spetsnaz eliminated Khan's henchmen and palace. On January 10, 1996 U.S. forces bombed Khan's "terrorist base" in Chandigarh as well as several other Augment bases in Serbia, Afghanistan, Iraq and Sudan. Facing certain defeat at the hands of combined forces from multiple nations, the very next day Khan and 83 of his Augment followers secretly escaped Earth aboard a stolen protoype vessel of the DY-100 sleeper ship christened the "S.S. Botany Bay". This ship was developed using technology reverse-engineered from the Ferengi ship that crashed at Roswell, and launched from the secret American facility nicknamed "Area 51." Khan headed for outer space with the dream of someday ruling a world of his own making. On board the ship, the crew were cryogenically frozen to allow them to remain in suspended animation.