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The Splinter Cell program was a black-ops training program created by theNational Security Agency's top-secret sub-branch Third Echelon. It was also the codename for an operational unit composed of lone field operatives called "Splinter Cells". The program produced and deployed units of highly-trained forward operators as the ultimate intelligence gathering force, with the support of a cutting edge technological team to retrieve information through traditional espionage techniques, but with 21st century military technology. Sam Fisherwas the first person selected into the program to operate in this role.

When critical intelligence could not be obtained by passive means, Third Echelon resolved the situation by conducting so-called "physical operations" — a euphemism for direct action. To do so, they introduced the "Splinter Cell" program, which was created to produce an elite recon-type unit comprised of highly-trained covert soldiers, who were then deployed to areas deemed either too sensitive or too risky for traditional entities such as the CIA or standard Special Forces. These agents then assessed and accessed information vital to the security of the United States.

These units, individually known as "Splinter Cells", were small, elite intelligence-gathering forces consisting of a lone field operative supported by a high-tech remote team. They were used in situations where more than one operative — even though highly secret — would arouse too much attention. They infiltrated secure installations, seized critical intelligence, destroyed dangerous data or equipment and neutralized the enemy as needed, without leaving a trace. The doctrine of Third Echelon was that although killing may compromise secrecy, "the choice between leaving a witness or a corpse is no choice at all".

The field operatives of the Splinter Cell program were very unusual people, even when compared with "ordinary" special operators or "ordinary" spies without official cover. They had extraordinary training and skill, were mind-numbingly precise, they dealt with grave stress and risk and were aware that a single mistake could be fatal to them. Due to the complexities of their operations, they underwent rigorous and very extensive additional training, beyond their special forces background. Stealth skills and hand-to-hand combat skills were stressed, due to the fact that they must remain invisible while conducting extremely close quarters covert operations. Splinter Cell operatives were capable of moving through areas completely undetected, by both human and electronic means.

Due to political concerns, sometimes triggering a single alarm could mean mission failure, depending on the importance of the particular mission at hand. When an enemy was encountered, these agents needed to be able to silence them quickly and quietly. They received excellent hand-to-hand combat training, which was vital when snatching specific targets or seeking to extract intel from guards. In close combat situations, Splinter Cells expressed great control and skill when applying such techniques. Their combat training was centered around remaining silent while engaging.

The original Splinter Cell program was conceived with a single field agent, although as of 2007, an NSA official indicated that at least two-man squads were being used. These agents have the ability to operate in a manner that is referred to as "Fifth Freedom" — the freedom to do whatever is deemed necessary to protect the Four Freedoms, seen as cornerstones of American moral thought, as defined in one of President Franklin D. Roosevelt's famous speeches. Roosevelt articulated these as "Freedom of speech, freedom of religion, freedom from want and freedom from fear." Under the (unofficial) Fifth Freedom, an operative could disregard any law, agreement or framework of ethical behavior in order to protect the previous four. For example, the operative could kill in combat or by assassination, torture or kidnap people, deploy on U.S. soil, spy on other U.S. government agencies, et cetera. The downside was that if an operative were captured or killed, the U.S. government would disavow them — either by claiming that the person has gone rogue or by denying that they even existed.

Mission objectives and locations varied, but a Splinter Cell's basic goal was to infiltrate the area of operations (AO), complete any objectives assigned and then extract without being detected. Special Reconnaissance (SR) was their core competency.

Third Echelon's Splinter Cell agents were sent to physically infiltrate dangerous and sensitive hostile locations to collect the required intelligence by whatever means necessary. Their prime directive was to conduct their operations while remaining invisible to the public eye. They were authorized to work outside the boundaries of international treaties, but the United States would neither acknowledge nor support their operations. Officially, Third Echelon and its agents did not exist.

Third Echelon's methods made use of "classical" methods of espionage powered by the latest technology for the aggressive collection of information. Splinter Cell operatives were recruited from the U.S. Special Forces communities of the Army, Navy, Marine Corps and Air Force. They were then shaped into the "ultimate covert soldiers": specially-trained individuals capable of not only working alone in hostile environments, but of doing so without leaving a trace. Like a sliver of glass, a Splinter Cell was small, sharp, and nearly invisible. Thus, Third Echelon, a sub-agency of the NSA, consisted of an elite team of strategists, hackers, and field operatives that worked together as a team to respond to crises of information warfare with the highest degree of secrecy humanly possible.