National Secessionist Forces

The National Secessionist Forces (NSF) is the second major organization to be encountered by the player in Deus Ex. During the early stages of the game, the NSF are depicted as a terrorist organization, who were partially said to be involved in numerous terrorist acts. However, the player later discovers in the game that many of these reported terrorist acts are lies, or they were framed by Majestic 12 for many of the terrorist acts. Many of the terrorist acts had been done by Majestic 12 as a plot to reduce support for the NSF and their allies. The NSF were also framed for many other criminal acts, including illegal drug smuggling (although the Luminous Path Triad, being a mafia group, is involved in such smuggling activities). When the NSF started running out of troops during their assault in New York City, however, they began to desperately take hostages, allowing them to stall for time and delay  UNATCO, despite a policy discouraging hostage-taking.

While the United Nations and the U.S. government classified the NSF as a terrorist group, many people saw the NSF as liberators from an increasingly authoritarian U.S. central government. Leon Woods was killed at his infamous last stand in 2045 at Squalnomie Square, but the NSF continued on gaining more and more strength, as well as gaining support from  Silhouette (the resistance movement against the French government), the Luminous Path Triad (a mafia group in Hong Kong), and X-51 (a group of former Area 51 scientists). Dissident computer scientists and programmers, said to be based in Seattle and San Francisco, aided the NSF in setting up a highly encrypted communication network, eroding the edge that  MJ-12 and UNATCO had due to their control over the Aquinas network and ECHELON. At this point, the United Nations declared war on the NSF. The state of Texas, which unsuccessfully tried to secede in 2032, is described in an email as being in a state of constant warfare between the NSF and UNATCO and the U.S. military. Their resistance to the U.S government makes them dangerous in Majestic 12's sight. Majestic 12 bomb the Statue of Liberty to justify the need to establish a UNATCO headquarters on Liberty Island with the (secret) intent of destroying The NSF to suppress the truth.

The NSF discover that the United Nations and the U.S. government are deliberately restricting the lower-class people from accessing Ambrosia, which is the  only known temporary remedy  for The Gray Death. The NSF learn that UNATCO is actually under the control of Majestic 12. The NSF fear that Majestic 12 will take over the world, so forcefully intercept an Ambrosia shipment and steal the vaccine in an  attempt that government employees and the lower class might be given the same chance as the upper class to survive. The NSF planned to load the Ambrosia onto a 747 where it could be shipped to Luminous Path Triad scientist Tracer Tong to be  synthesized, making the NSF popular with the lower classes.

JC Denton is sent by Joseph Manderley on orders of FEMA director Walton Simons to stop the NSF, but subsequently learns of the truth and allies with the NSF. He sends an NSF distress signal from NSF's New York headquarters in Hell's Kitchen, allowing other NSF bases and resistance groups in Europe to take necessary counter measures. Several prominent members from the New York Section remain at large, probably waiting to reform the organization in New York; indeed, this is evidenced by the  fleeing of NSF commanders Decker Parkes, Erin Todd, and Wayne Young to Europe. During the game, an NSF brigade is conducting operations in Paris under the command of Chad Dumier, leader of Silhouette  and the Illuminatus Morgan Everett. Morgan Everett, in conversation with JC, mentions their still-operational HQ as being a few hundred miles north of the X-51 base at Vandenberg. In Paris, JC Denton overhears a man asking his wife to come with him to America as he has been contracted to work with the NSF.

After the events of Deus Ex, most of the organization seems to be crippled but not destroyed. This is partly due to the actions of the player, whose short tenure with UNATCO saw the capture of several important bases, including the NSF New York  headquarters, capture or death of several commanders, including a prominent NSF leader and financial backer, Juan Ivanovich Lebedev, and the failure of a critical operation in New York City.