The lair is located on the map slightly north of the East Boston Preparatory School. It is behind a building that is unmarked, and near a warehouse that is 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, it is a new player character home.
The Mechanist's lair was in part originally a RobCo sales and 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 facility that pre-war 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.
A Vault-Tec lunchbox is located 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.
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.
In the security room overlooking the first decontamination corridor is an elevator that goes straight to the control room. It can be activated by shutting down the lockdown, which is done by entering the three supervisor holotapes, found in the lair, into the neighboring computer and manually overriding the lockdown.
Despite being another interior settlement, this has significantly more customization options than Home Plate, but will have a settlement building limit unlike Home Plate.
In most ways it behaves more like an exterior settlement, in that settlers can be moved here, and supply lines can be established. The most notable exterior settlement options missing are food resources and stores.
There are some patches of 'earth' on the top level in the northernmost corner, just outside the entrance to the facilities wing, where water pumps can be placed.
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.
pcxboxoneps4 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.
ps4 Using the cargo elevator immediately behind the original spawn point may cause robot companions to disappear, sometimes permanently. [verification overdue]
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]