A mothership uses the finest alien technology and possesses both offensive and defensive capabilities. It is protected by shield technology and its main weapon is a powerful raygun cannon named the death ray (this device, when used on Earth, resembles the power of a nuclear warhead), which connects to the lower section and can be used for both orbital strikes on a planet and combat against other space vehicles.
Passages between the various sections can be made faster with teleportation matrices installed in key points of the ship, which can be turned off in case of internal problems by the captain of the ship. It also possesses a large number of healing archways placed in all sections, that will heal and remove all radiation of anyone who walks through them.
A mothership also contains various laboratories for experimentation on living beings and technology such as biological research, experimentation labs and research labs. There is also a vast number of storage facilities in which items retrieved from a planet below are stockpiled, and abducted species are kept alive or are frozen for preservation, used for experimentation or targets for weapons.
Aside from living quarters for the crew and the bridge, the remainder of the vessel is dedicated to the ship's basic functions. The engineering core in the lower part of the ship provides access to most of the maintenance sections like the maintenance level, engine room or waste disposal. In the robot assembly, the various alien drones are produced and repaired. Death ray control and death ray hub are dedicated to controlling the mothership's main weapon. A mothership also features its own hangar in which other smaller alien ships can be stored and maintained.
It seems that the alien captain of the ship or some other ranking alien can broadcast itself throughout the ship as a hologram.
Companions will not follow the Lone Wanderer onto the ship even after beating the last quest. However, contrary to the previous add-ons, followers will wait next to the homing beacon upon boarding, with the exception being Dogmeat, as he returns to Vault 101.
Many of the chairs on the ship throw off a spray of blood when struck with a melee weapon. Unlike the aliens, the chairs bleed red.
When wearing the spacesuit, the left sleeve has been replaced by the Lone Wanderer Pip-Boy, with its trademark fingertip-less glove. This glove remains fingerless when the depressurization chamber is depressurized, even though this would cause considerable pain and swelling in real life.
Taking the spacesuit off during the space walk results in the Lone Wanderer's head exploding.
If Initiate Pek was saved at Falls Church, Paladin Hoss, the unnamed Paladin, and Pek may randomly appear somewhere on the ship. They will not aid the Lone Wanderer but try and reach the bridge to get back to Earth.
On one of the captive recordings (subtitles may be needed to see what it says) one of the captives, who is a high ranking officer, can be heard talking about how he has the codes for a part of the U.S.'s ICBM arsenal hinting that the aliens launched the United States' missiles at China. However, it's equally likely that the officer was merely offering the most sensitive information at his disposal believing it's what the aliens wanted, as the ability to clearly communicate specific questions to humans seems to elude the Aliens in many recordings. This is further supported by the fact that the death ray already gave the Aliens the ability to simulate a nuclear strikes, rendering the idea that they would need to hijack a nuclear arsenal moot.