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, 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 experimentations 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 the 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.
Earthly animals aboard the ship appear able to breathe, which suggests that the ship's atmosphere has sufficient amounts of oxygen, implying the aliens also breathe oxygen. However, the alien found at the crash site of Recon craft Theta is wearing what appears to be a pressure suit with a helmet. The latter may be explained in that the suit is either standard equipment or an individual garment, as evidenced by other aliens wearing the same suits, or meant for hospitable atmosphere if not otherwise available i.e. in an unpressurized area or if present e.g. Earth's atmosphere is not e.g. due to biological or radiological dangers.
Followers cannot follow you on the ship even after you beat the last quest. However, contrary to the previous add-ons, followers will wait next to the Homing Beacon when you board, 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 your Pip-Boy, with its trademark fingertip-less glove. This glove remains fingerless when you depressurize the depressurization chamber, even though this would cause considerable pain and swelling in real life.
If you take the spacesuit off during the space walk, your head will explode.
If you saved Initiate Pek at Falls Church, Paladin Hoss, the unnamed Paladin, and Pek may randomly appear somewhere on the ship. They will not aid you but try and reach the bridge to get back to Earth.
If you listen to one of the captive recordings ( there is a glitch, so you might need subtitles to see what it says) you can hear one of the captives who is a high ranking officer, talking about how he has the codes for the U.S.'s ICBM arsenal hinting that the aliens launched the United States' missiles at China.