Shadows of the Machine

"Shadows of the Machine: The Forces in Motion Between Deus Ex and Deus Ex: Invisible War" is the backstory for Deus Ex: Invisible War. The backstory appears in Deus Ex: Invisible War: Prima's Official Strategy Guide and tells of the events that occurred after Deus Ex and up to the beginning of Invisible War.

The "note" insert that appears in the transcript below is part of the original text.

Transcript
Starting with JC Denton's destruction of Area 51 in 2052, the world entered a period known as the Great Collapse. Depression and wars ravaged the landscape. The Illuminati lost all means of controlling nations and peoples, while JC and Paul Denton were powerless to protect governments from warlords and from the damage already done by the MJ-12 shadow government. Organizations with visions of a new world order had to bide their time for nearly two decades, during which they rebuilt their power and began vying for global dominance once again.

At the start of DXIW, the Illuminati have established the roots of political power with the use of two puppet organizations: the Order, a new church based upon an open-ended, unifying religious system and the WTO, a stabilizing socio-economic force. The WTO is led by Chad Dumier, the former leader of the Silhouette revolutionaries in MJ-12-controlled Paris. The Order is led by Illuminati heiress Nicolette DuClare, robed and veiled as Her Holiness. Together, Chad and Nicolette want to become the puppet masters of a rebuilt capitalist civilization. They hope to steal JC and Paul's nanotech research so they can centralize and expand the Illuminati's traditional, behind-the-scenes control.

JC and Paul have a different vision for humanity, one founded upon true freedom rather than the rhetoric of freedom employed by the Illuminati. They want to use biotech enhancement to raise everyone to near-perfect levels of health, productivity and mental acuity. A society of superior equals, they feel, will necessarily join together in harmony to shape a truly utopian civilization. To this end, they created an underground group called ApostleCorp, which has developed the enabling technology at secret facilities around the world. Unfortunately, ApostleCorp's leaders — JC and Paul — are both out of the picture as DXIW begins. JC, failing to merge seamlessly with the Helios Al at the end of Deus Ex, fell into a state of catatonia at a secret facility in Antarctica. Paul had to be cryogenically frozen at an ApostleCorp lab in Cairo, where he will remain until someone can figure why his body rejected a seemingly routine nanite-infusion.

A third organization, a radical off-shoot of the Order known as the Templars, blames the Collapse on the misuse of technology and wants to destroy all nanotech advances. The Templars believe themselves to be the devout, modern incarnation of the ancient Knights Templar but, in reality, they are a monster born from the Illuminati's own scheming, difficult for Her Holiness to control. Publicly, Luminon Saman, of the Order, leads a crusade to reform the Church. Privately, he is the leader of mobs who terrorize "modified" humans and the communities that accept them. He seeks to destroy you, ]C, Paul and all that they have created.

At the start of the game. The Templar Luminon, Saman, is very close to uncovering the secrets of ApostleCorp. He destroys the entire city of Chicago in order to wipe out the ApostleCorp facility where you have been in training as a bioenhanced covert operative. You and a fellow trainee, Billie Adams, are rescued just in time by the ApostleCorp leadership and taken to a sister facility in Seattle. But ApostleCorp falls victim to a double agent — Billie Adams is selling her knowledge to both the Templars and the Illuminati and both are preparing operations against the Seattle facility.

You take the role of Alex D, an MJ-12 experimental clone of JC and Paul Denton. You were "born" in a cloning chamber players may recall from their exploration of Area 51 in Deus Ex. In the first game, that cloning chamber was empty. In DXIW, it is revealed that the missing "Alex D" was removed from Area 51 at the age of five, shortly before the events of Deus Ex took place. Who took you is still a mystery. All anyone knows is that you were raised by ApostleCorp in Chicago and have the potential for biotech enhancement.

You begin the game oblivious to this power struggle. All you know is that you have been training to become a highly paid covert operative for a large corporation. You don't even know the names "ApostleCorp" or "MJ-12" — you spend much of the game exploring ApostleCorp and MJ-12 facilities, uncovering the truth about your past. Ultimately, you will have the chance to remain loyal to your creators or to reject their utopian vision. Ten billion (virtual) people depend on you to make the right choice for the future of world civilization.