There are 5 main levels of diagnostics

Level 5 Diagnostic: This automated procedure is intended for routing use to verify system performance. Level 5 Diagnostics, which usually require less then 2.5 seconds, are typically performed on most systems on at least a daily basis, and are also performed during crisis situations when time and system resources are carefully managed. 

Level 4 Diagnostic: This automated procedure is intended for use whenever trouble is suspected with a given system. This protocol is similar to Level 5, but invokes more sophisticated batteries of automated diagnostics. For more systems, Level 4 diagnostics can be performed in under 30 seconds. 

Level 3 Diagnostic: This protocol is similar to level 1 and 2 diagnostics but involves crew verification of only key mechanics and systems readings. Level 3 diagnostics are intended to be performed in ten minutes or less.

Level 2 Diagnostic: This refers to a comprehensive system diagnostic protocol which, like a level 1, involves extensive automated routines, but requires crew verification of fewer operations elements. This yield s a somewhat less reliable system analyses, but is a procedure that can be conducted in less then half the time of the more complex tests. 

Level 1 Diagnostic: This refers to the most comprehensive type of system diagnostic, which is normally conducted on ships systems. Extensive automated diagnostic routines are performed, but a level 1 diagnostic requires a team of crew members to Physically verify operation of a system mechanisms and to take system readings, rather then depending on the automated programs, thereby guarding against possible malfunctions in self testing hardware and software. Level 1 diagnostics on major systems can take several hours, and in many cases the subject system must be taken offline for all tests to be preformed. 

Alerts

Condition Green: It's the normal condition/operation of a ship. Condition green is initiated by the commanding officer (CO) or the first officer (FO). All systems go back to normal. All alert awareness lights go off, and an audible confirmation is issued. All crew shifts return to their normal rotations.

Specific systems preparations include:

• Level 4 automated diagnostic series are run on all ships primary and tactical systems at the beginning of each shift. Key systems may require more frequent diagnostics per specific operational and safety rules.
• At least one major power system to remain at operations status as all times. At least one additional power system to be maintained at standby.
• Long range navigational sensors to be active if the ships is traveling at warp speed. Lateral and forward sensor arrays to be maintained at ready status, although these instruments can be made available for secondary mission use at the discretion of Ops
• Navigational deflector to be active as needed for the protraction of spacecraft from unanticipated debris or drag from the interstellar medium. 
• At least 40% of phaser bank elements and one photon launcher to be maintained at cold standby status, available for activation at two minutes notice.
• One shuttle bay is maintained at launch readiness with at least one shuttle vehicle maintained at launch minus five minutes status

Yellow Alert can be invoked by the Commanding officer, Ops, CEO, TAC/SC, TAC/ASC or by the supervisor of any current primary mission operation. Additionally, the main computer can automatically invoke Yellow Alert status in some cases upon detection of certain types of unknown spacecraft, as well as upon detection of certain types of malfunctions or system failures.

Specific systems preparations include:

• Level 4 automated diagnostic series run on all ships primary and tactical system to determine ships current readiness status. 
• If presently off-line, warp power core brought to full operation condition and maintained at 20% power output. 
• Main impulse propulsion system brought to full operation condition. At least one backup reactor element is brought to hot standby. 
• All tactical and long range sensor arrays are brought to full operational status. Secondary mission use of any sensor elements can be overridden if required by the bridge. 
• Deflector systems brought to full standby. Secondary deflector generators brought to partial standby. All operational backup generators are energized to partial readiness
• Phaser banks are energized to partial standby . Power conduits are enabled, and targeting scanners are activated. 
• Photon Torpedo launchers are brought to partial standby. One torpedo device is energized to partial launch readiness and primed with a standard anti-mater charge, unless specifically overridden by Ops or Tactical.
• The Battle Bridge is brought to partial standby status and backup bridge crews are notified.
• Two of the shuttle-bays around brought to launch readiness. 
• Onboard sensors record the location of all personnel and alert Security of any anomalous activity. Location and activity information is recorded for post mission analysis. 

Red Alert : This condition is invoked during actual states of emergency in which the vehicle or crew are endangered, immediately impending emergencies or combat situations. 

During Red Alert situations, crew and attached personnel from all three duty shifts are informed via alarm klaxons and enunciator lights. Key second shift personnel are ordered to report immediately to their primary duty stations, while other second shift personnel report to their secondary duty stations. Key third shift personnel are ordered to report to their secondary duty stations in fifteen minutes. 

Red Alert situations, by their very nature, frequently involve unforeseeable variables and unpredictable circumstances. For this reason, Red Alert requires the Commanding officer and all personnel to remain flexible. All red Alert operating rules, therefore, are subject to adaptation.

Red Alert can be invoked by the CO, Ops, CEO, TAC/SC, TAC/ASC. The Computer might also bring the ship to Red Alert Status.

Specific systems preparations include:

• If presently offline, warp power core to be brought to full operation condition and maintained at 75% power output. Level 3 diagnostics on warp propulsion systems at initiation of Red Alert Status, Level 4 series repeated at 5 minute intervals.
• Main impulse propulsion system is brought to full operating condition. All operations backup reactor units are brought to hot standby. 
• All tactical and long range sensor arrays are brought to full operations status. Secondary mission use of sensor elements is discontinued, except with approval of Ops
• Deflector systems are automatically brought to tactical configuration unless specifically overridden by the Tactical Officer. All available secondary and backup deflector generators are brought to hot standby 
• Phaser banks are energized to full standby. Power Conduits are enabled, targeting scanners are activated. 
• Photon torpedo and Quantum Torpedo Launchers are brought to full standby. One torpedo device in each launcher is energized to full launch readiness.
• The battle bridge is brought to full standby status and backup bridge crews are notified for possible duty in the event of need.
• All three shuttle bays are brought to launch readiness. Two shuttlecraft are brought to launch status minus 30 seconds. 
• Level 4 automated diagnostics are preformed to verify readiness of autonomous survival and recovery vehicle systems. Readiness of ejection initiator servos is verified through a partial Level 3 semi automated check. Security officers are assigned to insure that all passageways to lifeboat accesses are clear. 
• Isolation doors and force fields are automatically closed between sections to contain the effects of possible emergencies. Including force and decompression of habitable volume.

External Support Mode: This is a state of reduced activity that exists when the ship is docked at a Starbase or other support facility. During External Support Mode, the ship will typically receive umbilical support for at least a portion of the operational power and/or life support, thus enabling a partial or total shutdown of onboard power generation.

External Support Mode rules permit the spacecraft to conduct a cold shutdown of all primary power plans as long as sufficient umbilical support is provided for all remaining personnel and systems. These protocols are intended to permit maintenance of critical systems, which would otherwise be difficult to accomplish during normal service cycles. 

External Support operational rules include:

• Spacecraft must be hard docked to support facility umbilical connects providing electro plasma system power, environmental support, structural integrity field power, and thermal and gravitation control At least one hard gangway must provide direct shirtsleeve access between spacecraft and the service facility.
• Cold shutdown of all primary power plants is permitted as long as sufficient umbilical support is provide for all onboard activity. It is preferred that at least one auxiliary fusion generator remain online, if possible.
• Partial shutdown of environmental support systems is permitted, allowing atmospheric and water processing to be handled by support facility through umbilical connects. Life support service must continue to be provided for all inhabited portions of the ships interior. On board ventilator fans, air conditioning, thermal control, and plumbing must be maintained, although specific areas may be shut down as needed for maintenance work.
• Gravitation power generation may be discontinued so long as field energy for synthetic gravity is provided through umbilical connects. 
• Cold shutdown of hot structural integrity field and inertial damping field is permitted so long as spacecraft remains hard docked to support facility. It is preferred that at least one SIF generator remain at hot standby.
• Cold shutdown of all navigational and tactical deflector systems is permitted so long as the spacecraft remains hard docked to the support facility.

Reduced Power Mode: Reduced Power Mode refers to a number of operating states designed for maximum power conservation. These protocols can be invoked in case of a major failure in spacecraft power generation, in case of critical fuel shortage, or in the event that a tactical situation requires severe curtailment of onboard power generation.

When Reduced Power Mode is invoked, a Level 5 systems analysis is performed for the entire spacecraft, with the results made available to the CO, the CEO, and OPS. The purpose of this analysis is to determine an overall energy budget for the spacecraft, to help plan power allocations that will minimize operational compromises. 

Additional rules are:

• If the spacecraft is not presently traveling at warp velocity, a cold shutdown of the entire warp propulsion system is to be performed.
• Main impulse propulsion system is to be brought to the minimum required to maintain onboard power usage. Backup fusion reactors are to be kept at standby, but should remain offline unless necessary at the discretion of the CEO
• Hourly energy budget and consumption reports to be made by Ops  to the CEO and the CO
• Spacecraft flight operations are to be conducted in a conservative manner. If warp travel is deemed necessary, speeds greater then integral warp factors are not allowed due to lesser efficiencies at faction warp factors. (I.e. it is permitted to travel at warp 2, or 3, but not 2.5 or 3.5)
• Inertial damping system and structural integrity field to be operated at minimum levels. Only one of each generator to be operational, unless system failure is believed imminent or unless tactical situations dictate otherwise. Accordingly, changes in velocity are to be kept to a minimum.
• All use of tactical and lateral sensor arrays for secondary mission sot be discontinued, except where deemed essential by OPS
• Deflector systems brought to minimum power. Secondary deflector generator s and backups brought to cold shutdown unless deemed necessary by the CO, CONN, or TAC/SC. Navigational deflector to be operated at minimum power.
• Phaser banks brought to cold shutdown unless deemed necessary by the CO
• Photon launchers brought to cold shutdown unless deemed necessary by the CO
• Shuttle bay operations are suspended unless specifically authorized by the CO. Any use of shuttle vehicles is to be conducted from either secondary shuttle bay.
• Crew status survey to be conducted by Security department with preparations for contingency evacuation of part of the ships habitable volume for environmental support conservation
• Environmental systems to operate at no more then 50% or normal levels. Ships compartments not in use to be sealed off for conservation of environmental resources
• Transporter usage is not allowed unless specifically ordered by the CO or a department head
• Turbolift system usage discouraged for all personnel. Activation of turbolift requires voice ID.
• Energy intensive recreational actives such as holodeck 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 or TKL rations.