All key Operating systems and subsystems aboard the USS Cobain have a number of preprogrammed diagnostic software and procedures for use when actual or potential malfunctions are experienced. These diagnostic protocols are generally classified into five different levels, each offering a different degree of crew verification of automated tests. Which type diagnostic is used in a given situation will generally depend upon the criticality of a situation, and upon the amount of time available for the test procedures.

Level 1 Diagnostic - This refers to the most comprehensive type of system diagnostic, which is normally conducted on ship's systems. Extensive automated diagnostic routines are performed, but a Level 1 diagnostic requires a team of crew members to physically verify operation of system mechanisms and system readings, rather 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 off-line for all tests to be performed.

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 operational elements. This yields somewhat less reliable system analysis, but is a procedure that can be conducted in less than half the time of the more complex tests.

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 10 minutes or less.

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 involves more sophisticated batteries of automated diagnostics. For most systems, Level 4 diagnostics can be performed in under 30 seconds.

Level 5 Diagnostic This automated procedure is intended for routine use to verify system performance. Level 5 diagnostics, which usually require less than 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.