Uplink happens before and in the same universe as Darwinia.
Dr. Sepulveda is actually one of the head researchers of Darwin Research Associates. After Revelation succesfully destroyed the Internet, Sepulveda is off to try and restore it as well as recovering their lost investigations, the Darwinians. Uplink happens after and in the same universe as Darwinia.
The "before" theory doesn't make sense; the hardware used in Darwinia, and the dates, place it in the pre-Uplink period.The Darwinians were lost in a separate incident, and recovered during the events of Darwinia. ARC attacked Darwin Research to steal the Darwinians' code, or perhaps specifically the red Darwinians' code, which was incorporated into Revelation. Arunmor was supposed to be the Big Bad in Uplink 2.
After all, at the end of the first game, they do have a program under their control running, in hidden form, on virtually every computer in the world. There was a gendercide of some sort
Why else do only men appear in the world government databases?