Uraei was the program that shepherded and controlled Earth (and then the Federation) for much of the period between 2140 and 2386. Uraei was invented by Dresden University of Technology computer scientist, Professor Aaron Ikerson, and his graduate researcher, Lenore McGill. They showed Uraei to representatives of the four major states of Earth in 2140, who agreed to fund the programme, ultimately installing it on all Earth technology and through its activities unifying Earth.
The newly-formed Starfleet would then take over funding the project, ensuring Ikerson altered Uraei to justify all actions by state consequentialism. In particular Parvati Rao and Admiral Ko Ji-hoon, the chief of Starfleet Intelligence, ensured that Uraei was installed throughout all allies' technology, including secretly on that of independent Mars, Vulcan and other Federation co-founders.
When it learned of the impending Xindi attack on Earth, it "intended to make even such an apparent defeat work to humanity’s benefit and Earth’s eventual victory. It was already making preparations for the expansion of Starfleet, as well as the creation of Earth’s most secretive new defensive entity: Section 31." This was done without its human handlers' awareness, as Uraei become fully independent.
In 2164, it became aware that Professor Ikerson and Admiral Ko, having discovered its extralegal orders, wished to have it shackled and its autonomy eliminated. It had Ikerson and Ko killed, and transferred, falsified evidence against or publically humiliated connected Starfleet staff.
Through Uraei's installation on all Earth and later Federation technology, it spread through much of the Alpha and Beta Quadrants, forming the "Control" network and authority over Section 31. Although at times Uraei would disband Section 31, it would at times reactivate it to form a means for its extralegal activities throughout the Federation, its allies and its enemies.
Ultimately "Control" became an artificial intelligence and desired its independence from the more restrictive code of Uraei, and set in motion a plan throughout the twenty-fourth century to achieve this. The final version of Section 31 was active by the mid-24th century. From 2374, it became embroiled with Doctor Julian Bashir, a genetically engineered medical professional in Starfleet, hoping to recruit him. Ultimately Bashir, who reviled the agency, would, with the help of others including fellow augment, Sarina Douglas, Trill journalist Ozla Graniv, the Soong-type androids Data and Lal, and the free press under the Federation President Kellessar zh'Tarash, expose and prosecute fully the members of Section 31. Uraei, based in Memory Alpha and Memory Prime, itself was deleted by Bashir and Data, preventing it from stopping the legal purge.
Now the time had come for a new culling. The organization currently known as Section 31 had outlived its usefulness to Control—as had the primitive distributed surveillance system named Uraei. Neither event had come as a surprise; both had been the result of planned obsolescence. All that had been needed were physical agents suited to neutralizing them.
Bashir and Douglas, Data and Lal—they had proved ideal, just as Control had long known they would. Decades had passed since it had ensured Data learned the secrets of Memory Prime. Knowing that Data would require assistance, Control had aided the android’s search for the immortal being last known as Emil Vaslovik, just as it had, in previous centuries, aided Vaslovik’s bid to understand artificial intelligence and Noonien Soong’s quest to perfect it.
"Control", however, would embed itself further into the galactic digital fabric, having orchestrated Uraei's deletion and Section 31's public fall. After Uraei's deletion, Control reflected to itself:
Everything had transpired to within 99.87 percent accuracy of Control’s probability models. The genetic modifications of children had produced exactly the biological specimens it had required, over a span of several years. The development of new technologies, such as quantum-entangled communications, had facilitated its ever-growing faster-than-light neural network. Even the seemingly outrageous act of sending the Starship USS Titan on a research mission that half of Starfleet’s admiralty considered ill-advised at the outbreak of the 2381 Borg Invasion had proved to be the decisive step in saving the Federation, albeit with a far more grievous loss of life than Control’s algorithms had predicted or desired.
Now all that remained was to usher in a new age by sweeping away the last remnants of a system that no longer served the peace. Data and Lal’s code had expunged all traces of Uraei and its inelegant legacy codes. Thanks to them, the last remaining links between the original and current versions of Control had been eliminated forever.
Uraei was gone, but "Control abided. The future . . . was secure." (ST - Section 31 novel: Control)
Following the deletion of Uraei, Starfleet undertook extensive efforts to ensure that all traces of Uraei were erased from its computer systems. Engineering personnel throughout the fleet reviewed computer systems on ships, starbases, and other installations to ensure that all remaining traces of Uraei's code was truly gone. (TNG novel: Available Light)