In X-Wing Alliance, the player is able to enter a hangar bay for reloading, repair, and make changes to their craft's configuration without penalty. This allows a player to dictate the flow of combat easier. The primary advantages are that the player can reload and repair damage inflicted upon them. If done properly, a pilot's ship's laser, shield, and beam power levels will be returned to the level they were set at the beginning of the mission. That is, if a craft starts a mission at two-hundred percent (200%) shields, enters a hanger with no shields; when the pilot enters the hanger and allows the craft to land, and re-orient itself; they will depart with two-hundred percent (200%) shields and restored hull integrity. This allows a pilot to quickly "lick their wounds'' without having to fly evasively. They may also reload warheads in the hanger, allowing them to more easily dictate the flow of combat when they exit. This also allows a single-occupant craft to make multiple warhead delivery runs against a target and inflict greater damage. It is important that the pilot understands that entering a hanger will not restore systems lost as a result of combat damage. Thus, if a craft has had its radar display rendered inoperative, it will remain so after the pilot departs from the hangar with repairs and for the duration of the mission.

In most of the standard X-Wing Alliance missions, you will have the ability to hyper back to your command ship to execute repairs and reload. While this option is available, it does not let you proceed at your discretion. While you hyper to your command ship, reload and repair, and hyper back to the combat zone, the combat zone is still hot and active. This is of concern to a pilot as he may find himself "bound" to a combat area due to the fact that he must protect a mission-critical craft or must complete a time-sensitive objective. It is therefore important that a pilot be aware of when such conditions will be imposed on him and also be aware of the availability to return to their command ship as you will always have the option to return to your command ship.