"John Smith", also known as David Reynolds, is the unknown and mysterious mastermind behind the September Attacks. He is wounded in the series finale by Jake. Later on it was revealed in the Comics that John Smith was alive and being held in Loomer Ridge Detention Facility.
After contacting Robert Hawkins, Jake Green and Hawkins rescue him from Loomer Ridge Detention Facility. With a tracking device implanted in his chest, Thomas Valente tracked him for a short time until Hawkins and Jake short the tracker out.
Smith takes Green and Hawkins to a bunker Smith maintained to obtain the Precipice, Smith's key to unprecedented access to the J&R/ASA network. Unbeknownst to Jake and Robert, entering the bunker tripped an alarm notifying Valente of them entering. Evidently, Smith was aware of this, and had an escape route prepared.
Valente attempted to take out Hawkins, Green, and Smith with a Predator Drone. The bunker is destroyed, but thanks to Smith's escape route, they all escape. Due to the destruction created at the bunker, Valente assumes Hawkins, Green, and Smith are all dead.