Mission 1: Pyrrhic Victory
When looking at the mission results for this first mission, it will say that Woods was saved. There’s no other way around it and if you don’t save Woods during the mission, the game ends. It’s more or less a red herring that there could have been a different outcome that may have happened, but there isn’t. There’s only one way through the mission and you aren’t given any choices during it.
Mission 2: Celerium
Much like the first mission, there is only one way through this one as well. Although the after action report may make it seem like you cannot recover the Celerium, you must to progress the story. Not doing so will end the game as a failed objective.
Mission 3: Old Wounds
Now is when the game starts to offer certain choices that will affect dialogue and game options. Your first major choice is during the interrogation of Kravchenko. You have the ability as Mason to either put a bullet in Kravchenko while he’s talking, or resist the urge by rapidly tapping the button. If you do plug him, you will not learn that there is a mole in the CIA. If you resist however, the later dialogue with Noriega will change to reflect that there is a known spy.