Colonel Henry Jacobson had been in charge of an investigation at Quantico in 1987 of the first sighting of The Beacon. Being an old family friend of Olivia Dunham, she pays him a visited after the arrival of a second Beacon.
Hesitating to talk about the Beacon, Jacobson strongly recommends Olivia to stay away from it. Reluctantly he informs Olivia of the strange happenings during his investigation, which ended as the Beacon literary vanished into thin air.
After Olivia leaves Jacobson, an unknown man forces his way into Jacobson's house, stuns him unconscious, and attaches him to an unknown device. Torturing Jacobson by electrical shocks, the intruder tells him to think about the woman visiting him about the Beacon. Finally the intruder gets what he wants - apparently, the device is able to read Jacobson's mind - and he shoots the Colonel again. ("The Arrival")