October 2009. As a part of the international War on Terrorism, the United States initiated an invasion of North Korea. While the insurgency was successful, leading the the capture of over two hundred key terrorist leaders, the remaining resistance struggled for one final strike at the superpower. With the element of surprise on their side, the battered North Korean army launched a full scale biochemical attack on the continental United States. The viral attack claimed the lives of over 6.8 million American citizens, crippling the superpower.

July 2010. Still suffering from the after-effects of the Korean biological attack, the United States turns to outside powers for assistance for its suffering people. Having had relations with an alien race, the Kiosafians, since the mid-1950s, America struck a deal with them. The alien race had always been fascinated with human warfare - Despite primitive technology, humanity had an exceptional talent at coming up with innovative and effective ways to kill each other with it. In addition, America had long possessed nuclear technology, something that had eluded the Kiosafian civilization. So America would assist in developing weapons technology for the expanding alien populace, based on their advanced technology. In exchange, the Kiosafians would begin to develop a cure for the viral infection plaguing the earthly nation. However, the aliens requested test subjects for this miracle medicine. America accepted, feeling they could sacrifice criminals, the homeless, the terminally ill, and the rest of the 'dregs of society' to what they deemed to be the greater good. This secret deal was referred to by the American government as Project Shadow, a name chosen to represent the utter secrecy that must be associated with the situation.

August 2010. The two parties begin their work to fulfill their negotiations. The American government begins to alter the advanced technology of the Kiosafians to produce weaponry and tactical equipment. Energy-based weapons and other new military equipment are rapidly developed and prototyped within the once abandoned Area 51 facility, and then are shipped off to the American military for field testing. Among the uses for this technology was for the arranged abductions. A branch of the American military, dubbed the Shadow Marines (due to their close ties with Project Shadow) are used to actually execute the kidnappings. Suspected terrorists, criminals, and other undesirables in society were captured in secret and returned to the government. They were in turn given to the Kiosafians, who used them in a series of grueling trial-and-error tests to discover a way to end the infection that had spread amongst the American people.

September 2016. The new military technology is released into general use. The American populace is outraged at the apparent priority issues among the government officials. They feel that the money spent on the military advancements should have been used for medical assistance for the suffering population. Many riots and rebellions break out, which are quickly quelled by the USST infantry and the Shadow Marines. The troublemakers are taken to Area 51, and transported as additional test subjects to the Kiosafians, as an easy way to silence them.

December 2016. The Kiosafians successfully develop the antibiotic for the American government. They request, however, that the United States deliver the technology before they deliver the antivirus. Worried about how much their already low public support would decrease if the military technology they had (apparently) spent so much money on had simply vanished, they negotiate further. They agree that a war will be staged between them. This will give the Americans a chance to deliver the technology under the guise of military strikes against the alien world ships. The aliens will then, after a time period, retreat, ending the false conflict.

January 21st, 2017. The war begins. The American soldiers are oblivious to the fact that they're being sent intentionally into a trap - Only a few select officers know the truth. Given this, the U.S. soldiers take the war seriously. In contrast to the plan, the unknowing military successfully brings down several Kiosafian capital ships. Viewing this as a deliberate move by the American government, the false battles escalate into real war. In one specific mission, a team of Shadow Marines is sent to destroy one ship's generator core. The ship, however, is due to return to Kiosaf, the alien home world, to deliver the stolen technology.

As Lieutenant Joseph Liberator, second-in-command of your Shadow Marines squad, you board the Kiosafian ship to take down the core. Unfortunately, your team is unaware of the ship's recent course change to liftoff. No longer is it necessary to destroy the vessel. Now you must fight for your life, the lives of many, and acquire the antivirus that lead you there in the first place.