Thompson was one of the many CBDC agents under the command of Gabriel Logan in the Colorado Mountains mission. Logan found him and John Ramirez in one of the many tunnels sections of the Colorado Interstate 70 being held hostages by two of Archer's man. Logan saves both him and Ramirez and goes with them to the end of the tunnel while facing some Agency soldiers on the way.
When they reach a bridge beetwen the tunnels, Logan tells them to head to the first tunnel where he found Chance and get off of the mountains, unfortunately Steven Archer's chopper shows up and explodes the bridge separating Logan from both agents. Later in the Agency Bio-Lab mission, Logan Finds Ramirez being held in a cell and asks him about the survivors, Ramirez says only he and Jason Chance survived the Colorado Mountains. Meaning that Thompson died in the explosion of the bridge.