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Starships generally have a double structure in place, with a formal crew rank system in place to delineate the relative command of each crewmember. In addition, their will be an immediate, functional "bridge" crew in charge of the ship to keep it operating for a period of time. That is, the formal ranking system will have a single, overall captain of a ship. However, the captain cannot possibly be active and in control of the ship at all times... he needs a nap now and then. Several shifts are devised so there is an active captain of the current bridge crew controlling the ship at all times. Each crew position will likewise be filled on the basis of several shifts.

Ship crews are most often trained and organized by functional departments, which can include command and decision making, navigation and propulsion, communications, the sensing and coordination of information, and the operation of offensive and defensive systems, as well as duties not immediately critical to the functioning of the ship, such as security and research. 

In the days before the advent of Neuralinks and fly-by-neuron control of starships, a large dedicated staff would handle the operations of each functional department, bringing the whims of the command crew to life. Neuralinks and automation very severely reduced the need for huge physical crews.

Bjaki Crew Structure
An example of starship command structure, from the Bjaki Federation.
Each ship will generally maintain four Watches, or sets of bridge crews. They will maintain a rotation that allows the crews to work regular shifts for 3 days, then have 2 days off. During a rotation, there will be 3 active Watches (Command Watch, Second Watch, and Third Watch) and a Swing Watch who are on their days off. The Command Watch includes the Ship's Captain and Mate.

The Bjaki formal rank system consists of:
Fleet Admiral

Oversees entire fleet, sets policy and develops strategic action plans. Primarily a political position run from an office.

Oversees branch or section of fleet, promoted as necessary to maintain oversight and maintain an effective command and decision making process. Ensures the Fleet Admiral's directives come to pass. Primarily a political position run from an office.
Commodore Oversees a small branch of fleet. The position entails a lot of supply, provisioning, and paperwork duties rather than immediate decision making. A political position run from an office.
Group Captain Physically and directly commands an operational group of starships. The Group Captain is the man in the field, translating the strategic commands from a Commodore into the tactical actions of a group of starships. His position is carried out onboard a starship, in the thick of the action.
Captain Commands an individual ship. The position of Captain generally implies a larger, relatively important ship.
Commander Replacement watch captain or captain of a more minor ship.
Specialist Replacement commander, specialist in a particular ship's system and its relation to the ship as a whole. They are a leader among those actively working within their specialty and are expected to pursue improvements and new knowledge relating to the system. They are actively being trained in command.
Aspirant Junior specialist who is learning everything about the systems they have chosen to work with. They learn not only theory and operation but are being trained in how their systems relate to other ship's systems and how specific leadership skills affect ship operation.
Ensign Lowest officer rank. The Ensign has become dedicated to a specific set of systems within a starship and is beginning to learn advanced tasks.
Able Hand High Enlisted. Will perform routine or specialized duties in one particular area of ship function, like operating weapons subsystems during combat or operating drives during travel. The tasks involve a certain amount of specialization by the Able Hand but they still may have the ability to move between functional areas to further determine where their abilities best serve the ship.
Technician Low Enlisted. Will perform routine duties in one particular area of ship function, like maintaining weapons or drives. The simplicity of tasks provides the Technician with the mobility to be moved between functions easily in order to determine where they best fit on a ship.

Beyond the formal rank system, the ship's captain will create long-term and short-term plans for the ship's activities. The bridge crew is called the "Watch" and is staffed by one of four interchangeable watches according to a schedule created by the Captain, who also provides a Day Plan for the ship.

The Watch, depending on the ship, will generally consist of:
Command of the Watch The functional decision maker for the ship for the duration of the watch. In times of crisis, this position generally reverts back to the Captain.
Mate of the Watch The second in command, charged with coordinating and ensuring the CoW's orders become reality.
Watch Helmsman Senior Helmsman, in charge of ship navigation and course. 
Lee Helmsman Junior Helmsman, in charge of assisting the Watch Helmsman, carrying out routine Helm chores, monitoring drive systems, and anticipating and performing many of the calculations required by the WH. 
Situation Officer Senior Situations officer for the watch, in charge of collecting and organizing information for the ship's sensors and scanners and running the ship's defences and communications. 
Watch Tactical Action Officer Junior Situations officer, responsible for the ship's weapons and for assuming routine tasks assigned to the Situation Officer. 
Watch Quartermaster Junior command officer, responsible for assisting and coordinating other stations and for performing various tasks and calculations.
Flight Control Officer Responsible for coordinating the launching, retrieval, and operations of launched craft. 
Watch Proximate Head of on-board security, troops, and ground forces. A member of the Proximate Arm, or ground force, of the Bjaki Federation rather than the High Aegis starfleet.

They represent several departments, both in terms of functional departments and career track:
Command The portion of the crew dedicated to devising and initiating strategy, organization, and decision making. The bridge crew includes, descending, the Command of the Watch, the Watch Mate, and the Watch Quartermaster.
Helm The portion of the crew dedicated to manoeuvring the ship and overseeing the ship's drives and power systems. The bridge crew includes, descending, the Watch Helmsman and the Lee Helmsman.
Situations The portion of the crew dedicated to running the ship's sensors, scanners, and communications systems as well as the ship's offensive and defensive equipment. The bridge crew includes, descending, the Situation Officer and the Watch Tactical Officer.
Flight Control The portion of the crew that deal with coordinating outcraft activities. The Flight Control Officer is the only Flight Control representative on the bridge.
Proximate Arm The Aegis ground-forces, run as a separate arm of the military, dedicated to security, boarding actions, and ground manoeuvres. The sole acting member of the bridge crew from the Proximate is called the Watch Proximate. There may be other security forces on the bridge from the Proximate Arm but only the Watch Proximate acts in an official advisory role.