With Chaos Theory, the Splinter Cell series had worked out the last few bugs in its system. Fisher finally had a few moves he should've always had, such as a trusty knife and a reliable, instantly-incapacitating non-lethal attack. More importantly, the enemy AI was no longer equipped with bat-like sonar (note... exaggeration), which had made Pandora Tomorrow's single-player mode such a chore to play through.
Thus, Double Agent's single-player mode does not tinker with Chaos Theory's formula. It does offer a few new features, such as the occasional presence of an AI companion, allowing the use of moves previously seen only in the cooperative multiplayer mode, and the ability to piledrive an enemy combatant through the frozen ice under your feet. Its greatest innovations, however, relate to its story.
As Double Agent begins, Sam Fisher has hit hard times. A mission in Iceland goes wrong at the last minute, leaving a known terrorist on the loose with the formula for an explosive called Red Mercury - a substance that can be used to make a two-kiloton bomb the size of a baseball. Fisher is extracted from Iceland, only to find out that his daughter Sarah is dead, the victim of a hit-and-run.
Ten months later, Fisher has landed in a Kansas prison. As far as most of Third Echelon is concerned, the death of his daughter drove him mad with grief, and he's now paying the price.
Only Lambert, at first, knows the truth. With absolutely nothing left to lose, Fisher volunteers for the most dangerous mission Third Echelon has to offer - infiltrating a terrorist organisation, the JBA, so he can get close to its leader. To keep his charade intact, Fisher may have to compromise every moral he has left... or he might wind up sympathising with the terrorists' cause. Stirring stuff.
As you progress through Double Agent, you'll encounter multiple decisions, each one carrying immediate consequences. Act too much like a terrorist, by killing civilians or police officers for example, and Fisher might wind up joining them; act too much like a federal agent, and you'll blow Fisher's cover. You can track your trust level with either faction using your handy PDA, and depending on what side you've chosen, you'll unlock various stages, as well as change the course of the mission you're on.
For example, in the second level, you're tasked with getting in with a fellow convict who wants to eliminate another prisoner. You can opt to kill the prisoner for him or not. Doing so will earn the convict's trust, at the cost of the NSA's regard; not doing so will keep Fisher in good with the NSA, but the distrusting convict will prevent you from obtaining a gun shortly thereafter. Now you get to take on a prison full of armed guards with your bare hands. Decisions, decisions.
In Double Agent, you have to maintain a balance of trust between the NSA and the JBA. A primary objective will always shift your allegiance to a significant degree, so you have to make sure to counterbalance that by pulling off enough bonus objectives for the opposing side. If you get too cosy with either faction, you'll be given a special objective that must be completed within a limited time, or your mission is over.
Other new quirks see Fisher unable to fall back on the high-tech arsenal he's enjoyed in the past. Terrorists, after all, just don't have the same budget as a well-maintained Splinter Cell. He won't always have his trademark nightvision goggles, let alone his special rifle ammo or tricked-out pistol, while Fisher's outfit will change from level to level. Your current faction standing will also determine what's available for your starting arsenal.