Interested in the game's background? This section details the epic events leading up to the game's storyline, including the critical events vital to the flow of the story. Once you beat the game on Agent you'll be able to read up on the background through the character personnel terminal (in Grimshaw's office), so don't read on if you want to find it out through the game yourself as it does contain spoilers for the main plot.
Millions of years before the present (2023), a large alien vessel was scuttled on the bed of the Pacific Ocean. This alien ship possessed a special weapon on board - the weak nuclear force de-coupler - a dangerous weapon capable of tearing the molecules of atom bonds apart. Aware of watchful eyes waiting to get their hands on this weapon, an escape pod was dispatched to the alien ship's home galaxy while major sections of the ship were disabled and destroyed to ensure that this Cetan biological vessel would serve no threat to the universe.
Close to the year 2000 BC, another advanced alien lifeform - the Maians - discovered life on Earth as well as great potential, but decided to let humans develop undisturbed. Soon after in 1650 AD the Maians encountered another lifeform - the Skedar - who were bent on fighting and soon an all-out war began between them. After hundreds of years of fighting, an uneasy cease-fire developed. Skedar fanatics continued to fight the Maians however, who refused to surrender. Mankind continued to develop, but the Maians watched with disappointment at the wars and violence that technology brought forth. They continued to hide themselves, as they believed the act of revealing themselves may make things worse on Earth.
In 1985 the scientist Daniel Carrington discovered the Maians and contacted one of their vessels in orbit around Earth. The Maians developed an interest in Carrington and decided to introduce their technology to Earth through his "Research and Development" projects. Thus contact between Maians and humans finally began.
Then in 2006, the Skedar discovered the Cetan message pod and found the location of the alien ship - Earth. They began to study Earth in rather violent ways, by abducting people to discover the location of the ship. Eventually they pin-pointed it on the floor of the Pacific Ocean, but to reach it they would need the humans' help. They studied the largest technological corporations and decided that the company at the top of the list - the dataDyne Corporation - was best suited to help them reach their prize. They contacted Cassandra De Vries (the head of dataDyne), and proposed a deal that sounded too good to be true - which actually was. She agreed to assist them in exchange for advanced technology, and so dataDyne began construction of an artifical intelligence to help in the recovery operation.
Cassandra contacted the head of the NSA, Trent Easton, to "request" that he receive permission from the US President for the loan of a deep-sea research vessel. His subsequent requests were continually turned down. dataDyne and the Skedar could not steal the vessel without attracting the attention of the US government, so instead they planned to replace the President with a clone under their control. This extra work for Cassandra and Trent gave the Skedar another excuse to grant them more rewards, although little did Cassandra know that the Skedar intended to double-cross them all and test the Cetan weapon on Earth before wiping out the Maians.
Unfortunately for dataDyne and the Skedar, the sapient AI they had built to crack the codes of the Cetan ship had developed morals of its own and decided that this assignment was far too unethical and so refused to perform any further tasks. Cassandra ordered that his personality be removed, but before they could take action the sapient adapted the name Dr. Caroll and contacted the Carrington Institute, pleading for their help...