In the first Splinter Cell game, Sam was a retired Navy SEAL who was recruited to become a Splinter Cell operative for the National Security Agency’s (NSA) super-secret spy agency, Third Echelon. Think of him as another Solid Snake. Stealth infiltration is his professional trade, but he doesn't walk into missions unarmed, and he likes to hang from ceilings a lot. Since his recruitment, he’s prevented nuclear war, biological terrorism, posed as a criminal to infiltrate a terrorist organization, and stopped a Presidential assassination. Not a bad resume.
After the events of Double Agent, he had a falling out with Third Echelon due to playing the part of a terrorist so well that no one knew which side he was on anymore. Sam disappears and eventually takes it upon himself to investigate the “accidental” death of his daughter, leading him to the events of Splinter Cell: Conviction.