A mothership uses the finest alien technology and possessing 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.
On the PC version, it is possible to restore access to the "inaccessible" doors after the main quest is completed by using console commands. Go up to one of the disabled doors, hit the tilde (~) key to enable the console window, and click on the door so its Form ID pops up. Then type in disable, hit enter, then enter enable and exit the console window. The door should now be restored.
Another way to use the inaccessible doors is to target one while the console is open and enter activate. It will work if the door is supposed to move player to another map. If the door merely blocks a part of the same map, try entering unlock.
Using the method above to access the inaccessible door will result in being unable to get back to the Bridge. To fix this, open the console, type prid X (with X being the aforementioned Form ID), enter, then type enable, enter. You should be able to get back to the Bridge, but the inaccessible doors will become inaccessible again.
After killing the alien captain and finishing the quest This Galaxy Ain't Big Enough..., the player becomes de facto captain of the ship, but all remaining aliens (except 3 aliens in the steamworks) on board will still be hostile toward the player and any non-alien non-player character.
The Lone Wanderer, other humans, and creatures of the Earth aboard the mothership are able to breathe which indicates that the atmosphere of the ship has sufficient amounts of oxygen. This suggests the aliens could themselves breathe oxygen which is ventilated through the ship (despite that the alien found at the crash site of Recon Craft Theta is wearing what appears to be a pressure suit with a glass helmet). The latter may be explained this way: the suit is just meant for space flight or extra vehicular activities, to provide the alien with oxygen in case the Earth's air is not breathable to him, a precaution of cabin decompression, to stop the alien breathing in pathogens to which he is not immune, or because the aliens may have detected radiation levels on Earth.
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.