The Mechanist's lair was hidden underneath a RobCo sales & service center which primarily sold and maintained terminals. Employees of the service center were told specifically not to interact with any abnormal crates, or else they would be "taken to see our friends below." In a storage room for the center, a large door which requires an M-SAT to enter leads into a large underground pre-War facility that was used for the development & construction of robobrains (jointly run with General Atomics and the United States Army Robotics Division). Part of it functioned as a pseudo-prison which housed prisoners, who were later operated upon to remove their brains. After wiping their brain of memories and passing assorted tests, the brains would then be housed in a robobrain head and mounted to any of a number of devices, including the bodies of a normal robobrain, controlling stretchers or even controlling operations inside the control center.
Sometime before the events of Automatron, Isabel Cruz discovered the facility while scavenging and took it upon herself to use it to create an army of robots to save the Commonwealth from anything which may hazard humans.
The lair is located on the map slightly north of the East Boston Preparatory School. It is behind an unmarked building, and near a warehouse by a bridge and a small wharf. A freight elevator inside the building (enter the door named "garage") will take the Sole Survivor directly to the underground location. Upon completion of the add-on, the location becomes a new settlement.
A Vault-Tec lunchbox - By a skeleton at the end of the robot storage area (underneath a yellow eye protection poster). Another is located behind the generators at power substation B on a red stepladder.
Day Tripper - One floor above the desk which contains the Mr. Handy model. It's on the left desk which has a dead researcher in front of it.
The area with the overhead conveyor lines spawns robots on the spot, each with a chance of being a legendary robot generating a new legendary loot result each time the game is loaded here. However, only a limited number of robots from each line (3?) can be knocked down before they stop production.
Outside of the Mechanist's bedroom is a small button on a coffee machine which opens up a hidden door at the end of the hallway. The room contains a terminal, missile launcher, missiles, locked safe and a few packets of Mentats in a drawer. It is possible to lock yourself in this room.
This is one of the few interior locations which can be fast traveled to and from.
The exterior door cannot be opened until the quest Restoring Order is active.
After entering the facilities wings, continue until reaching the descending grated ramp. On the left, jump onto the ledge and over the pipe, one will find a Jangles the Moon Monkey and a cymbals monkey appearing to play pong while drinking two Nuka-Cola Quantums.
PCPlaystation 4Xbox One After completing the final quest, leaving the building may cause the game to crash. [verified]
Fast traveling directly to another location, rather than leaving through one of the doors, may solve the issue.
PC There is a chance for a saved game that the Mechanist's Lair cell may become graphically glitched when facing certain directions. Textures may pop in and disappear as you angle the camera and FPS drops dramatically when looking in that direction. There is unfortunately no known fix for this issue so far. The only way to circumvent this is by starting a New Game and hope for the best. Note that this issue does not make it impossible to finish the quest but makes it really tedious. (Tested on version: 1.5.157, Automatron and Far Harbor installed) [verified]
Playstation 4 Location and power armor locations can appear in the incorrect location on the map when inside the Mechanist's lair. This is corrected upon leaving the building. [verified]