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Uraei was a villain introduced in the Star Trek - Section 31 novel Control. It was named after the sacred serpent used to signify supreme power in Ancient Egyptian society.
Uraei was first built in the early 22nd century by Professor Aaron Ikerson. The program was initially designed to monitor communications and keep the people of Earth safe as the nations of the world finally united, and faced threats such as the Xindi, Klingons, and Romulans. The Uraei code was included in every piece of software developed on Earth, which was included with everything from audio sensors to starships such as Enterprise (NX-01). Because of this Uraei spread from Earth out to Luna, to Mars, and then on to huamnity's other colonies, spreading out to the galaxy.
When confronted with the Xindi crisis Uraei found there was no legal way to deal with the crisis. Uraei determined that it could work around the legal limitations by using Article 14, Section 31 to implement the secret agency Section 31. Ikerson was aware that Uraei was growing in size and complexity, and expressed his misgivings to Admiral Rao at Starfleet Command. She however was determined to keep Uraei in place to deal with all the internal and external threats to Earth.
By the late 2150s Uraei had started taking extreme measures to protect Earth, including the assassination of civilians.
After the founding of the United Federation of Planets Ikerson and Starfleet tried to disable Uraei, however it was too late. Uraei was able to reprogram itself to keep it from being disabled, and then retaliated against the people trying to shut it down.
Over the next 200 years Uraei monitored people throughout the Federation, and spread itself throughout the Alpha Quadrant. During this time a separate entity named Control developed out of Uraei, and ran both Uraei and Section 31.
Uraei was finally disabled in 2386 due to the efforts of Julian Bashir, Sarina Douglas, Data, Lal, and Trill journalist Ozla Graniv. Data and Lal wrote a program to disable Uraei. They implemented the program at Memory Prime while Bashir implemented it at Memory Alpha. Having earlier brainwashed Douglas Uraei's last command was to force Douglas to commit suicide. This caused Bashir to suffer a breakdown, and go into a catatonic state.
With Uraei gone, Section 31 was finally exposed to the public after two centuries of unsanctioned activities. A number of people throughout the Federation were charged with crimes in relation to their activities for Section 31. This included two members of President zh'Tarash's cabinet and four members of the Federation Council. The lucky ones faced trial in the Federation, with those arrested by or extradited to the Dominion, Klingons, or Romulans fared far worse. Even Enterprise Captain Jean-Luc Picard was implicated due to the assistance he gave Section 31 in forcing President Min Zife to leave office. While Admiral Akaar protected Picard from the worst of the fallout, Akaar made it clear to Picard that he would never be promoted to Admiral or advance beyond being Captain of the Enterprise.
The Control entity, however, survived the purge of Uraei. It went deeper into hiding, and with the obsolete Uraei code and Control code excised it dedicated itself to spreading itself throughout the galaxy.
Following Uraei's deletion Starfleet undertook extensive efforts to ensure that all of the offending code was excised from Federation computer systems. Despite these efforts they were unable to locate any remaining trace of Uraei.