JoGribbs

The game starts and Sam has left 3rd echelon after his daughter died and he was forced to murder Lambert during Double Agent. Grimsdottir leads Sam to Kobin, and Kobin reveals that 3rd Echelon paid him to supposedly kill Sam's daughter. The 'meeting' with Kobin was actually a trap to capture Sam by 3rd Echelon. We find out from Grim in america that the new head of 3rd Echelon, Tom Reed, is up to no good, and she is actually a mole inside 3rd Echelon for the president. They want you to stop Tom reed since you're technically not a part of the US government and you can work your way from the outside. 
 
Grimsdottir reveals that you daughter is alive, and you get a message from her part way through the game, but the principle twist isn't until later.  

The rest of the game kind of follows your attempt to stop Reed, until you go to Grimms office at third echelon. Here she reveals that it was your old handler, Lambert, who plotted to fake Sarah's death. he discovered that there was a mole inside 3rd Echelon, and that somebody was going to try and kill Sarah Fisher. He ordered Kobin to kill somebody that looked like Sarah to trick Sam. He did this because he wanted to keep Sarah safe, by making her think Sam was dead, and to make sure Sam would remain at third Echelon, thinking it was a random hit and run rather than an assassination.
 
So Sam finally confronts Reed, and he reveals that there's an international organisation that he's working for called Meggido (you hear the name earlier in the game, but you only learn what it means here). They wanted to kill the president so that the Vice President, who was sympathetic to their cause would take over. Reed wanted to kill the President because she wanted to get rid of 3rd echelon. Sam also figures out that it was Reed who was the mole Lambert couldn't find in third echelon.