Gameplay
As part of the JBA, Sam must complete objectives set by them to gain their trust as well as complete objectives from the NSA. The decisions he has to make will become increasingly difficult as he progresses through the game. Earlier decisions, such as deciding whether or not to free all of the prisoners during the prison breakout, will just affect his score, but as the game progresses, Sam is faced with serious choices that could kill thousands if made wrong, but may blow his cover if he does not do it.
Despite this, Sam must make the JBA trust him. If he is seen in restricted areas before, it will dramatically affect his trust with the JBA. Similarly, if he is caught using an NSA gadget or picking a lock in JBA HQ, his cover will be blown on sight.
He is also watched by the JBA in most of his missions, if he is seen completing NSA objectives or is thought to be doing something out of the ordinary, his trust will go down. Killing people apart from those ordered to be taken out will affect his NSA trust in the same way.
Read more about this topic: Tom Clancy's Splinter Cell: Double Agent