Cruise Mode: Normal operating condition of the ship.
 * Three working shifts maintain all primary operations at all times.
* Level 4 automated diagnostic series are run on all ship's primary and tactical systems at the beginning of each shift.
* At least one major power system to remain at operational status at all times and at least one addition power system to be maintained at standby
* Long range navigational sensors active if traveling at warp speed.
* Navigational deflector active as needed.
* At least 40% of phaser bank elements and one photon torpedo launcher to be maintained at cold standby status and available for action at two minutes notice.
* At least one shuttle maintained at launch readiness at launch minus five minutes status.

* All personal are informed of possible emergency action.
* Second shift crew are alerted to prepare for possible duty on five minutes notice.
* Level 4 automated diagnostic series run on all ship's primary and tactical systems to determine ship's current readiness status.
* warp core brought to full operating condition and maintained at 20% power output if not in currently in use.
* Main impulse system brought to full operational condition.
* All Tactical and long-range sensor arrays are brought to full operational status
* Deflector systems brought to full standby.
* Targeting scanners activated. Phaser banks are energized to partial standby. Photon torpedo launchers are brought to partial standby with one torpedo device being energized to partial launch readiness and primed with a standard antimatter charge unless overridden by Ops or Tactical.
*On board sensors record the location of all personnel and alert security of any anomalous activity. Location and activity information is recorded for post mission analysis.
* Level 5 automated diagnostics performed.
* One shuttle craft is maintained at launch readiness.

Yellow alert can be invoked by the Commanding Officer, Operations Manager, Chief Engineer, Tactical Officer or by the supervisor of any current primary mission operation. Yellow alert is always activated when communications with another ship cannot be established even if that ship is a Federation ship. (Star Trek II)

Separated Flight Mode: A set of operating protocols used when the Saucer module has separated from the Stardrive section.

Separated Flight Mode: For those ships that have the ability to separate the saucer section from the main drive section this is the mode that is initiated to prepare for separation.
 

* Level 4 automated diagnostic is run at the beginning of each shift.
* At least one major power system to remain operational and at least one to be maintained at standby.
* One shuttle maintained at launch readiness minus five minutes. Once separation is ordered the following rules are observed.
 

* Warp power core brought to full operating condition and maintained at least 90% power output. Level 3 diagnostics conducted on warp propulsion at initiation of Red Alert Status and level 4 diagnostics repeated at 5 minute intervals.
* Main impulse propulsion brought to full operating condition.
* Saucer Module SIF/IDF systems are set to high output for all velocity regimes, including low warp or sublight velocities.
 

* If not traveling at warp speed a cold shutdown of the entire warp propulsion is performed. Exceptions are when the warp core is the only remaining power source or is expected to be due to other system's immanent failure.
* Main impulse brought to minimum required to maintain onboard power usage. Backup fusion reactors kept at standby but should remain offline.
* Hourly energy budget and consumption reports are made by Operations Manager to the Chief Engineer and CO.
* Flight operations are conducted at a conservative manner. If warp speed is necessary speeds greater than integral warp factors are not allowed due to lesser deficiencies at fractional warp factors (i.e., it is permitted to travel at Warp 2.0 or 3.0 but not Warp 2.5 or 3.4).
* Inertial damping system and structural integrity field to be operated at minimum levels. Change in velocity to be kept at a minimum.
* All use of tactical and lateral sensor arrays for secondary missions to be discontinued, except were deemed necessary.
* Deflector systems brought to minimum power. Secondary deflector generators brought to cold shutdown.
* Phasers and Torpedo launchers brought to cold shutdown.
* Shuttle bay operations suspended. Ingress and egress is to be minimized, with use of force field doors minimized.
* Crew status survey to be conducted by Security department with preparations made for contingency evacuations of part of the ship's habitable volume for environmental support conservation.
* Environmental systems operating at no more than 50% capacity. Ships compartments not in use to be sealed off for conservation of environment resources.
* Transporter usage not allowed.
* Turbolift system usage discouraged unless absolutely necessary. Activation of turbolift requires voice ID verification.
* Energy-intensive recreational activities such as Holodeck usage not permitted.
* Food replicator usage is not allowed. Preserved food stores are made available to all personnel. In a lesser crisis minimum replicator power can be made available for synthesis of TKL rations or similar.
* Any of the following protocols can be disregarded if the CO deems it necessary.


Sources:
Star Trek: The Next Generation Technical Manual by Rick Sternbach and Michael Okuda. © 1991 Paramount Pictures.

The Star Trek Encyclopedia: A Reference Guide to the Future by Michael Okuda and Denise Okuda with Debbie Mirek. © 1994, 1997, 1999 Paramount Pictures.