When the synths launched their attack on the Switchboard, they successfully breached the doors within 30 seconds and began shooting at everyone within. With both coursers and Generation 1 and 2 synths attacking, many Railroad members fled through the HQ's escape tunnel. Agent Tommy Whispers successfully secured the base's supplies, but was killed in the process. Tinker Tom activated their automated turrets, but they proved to be of little use against the advancing synths.
At Augusta safehouse, two coursers led the assault, killing virtually everyone. Agent Blackbird was the only survivor, but couldn't locate the rescued synth that the safehouse was protecting. The synths also attacked and destroyed safehouses Allen and Herkimer.
Following the loss of the Switchboard, the surviving members of headquarters were forced to relocate to underneath Old North Church, where they set up the Freedom Trail for others to find them. The losses they incurred resulted in them being undermanned, with Agent Glory having to run constant missions to fill in for the deceased Tommy Whispers. They also did not have the resources needed to train any further agents.
Randolph safehouse discovered a nearby force of synths and chose to cut all contact with the other safehouses. The loss of contact with Augusta, Allen, Herkimer, and Randolph led headquarters to regretfully declare that all four safehouses were destroyed by synths. Agent Blackbird failed to make contact with the rest of the Railroad and was later captured by raiders and killed.