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The way that the auto destruct sequence has been activated on starships has changed over time, as was the way the destruct sequence was carried out.
The sequence on the original Constitution class vessel was begun by tying in the ship's main computer to the bridge. The Captain would then identify himself to the computer, and provide the first code - which was One-One-A. The First Officer would then identify himself to the computer, and provide the second part of the sequence - which was One-One-A-Two-B. Then the Chief Engineer would then give the third part of the sequence - which was One-B-Two-B-Three. The computer would then announce that the sequence had been completed and engaged. It would then request the final code from the Captain. The Captain would again identify himself, and give the final code, which was Zero-Zero-Zero-Destruct-Zero.
At that point, the computer would begin a thirty second countdown. The self destruct sequence could be cancelled at any time from thirty seconds down to five seconds. However, after the five second point had been reached, the destruct sequence could not be stopped. If it was to be cancelled, the Captain would identify himself to the computer. He would then give the abort auto-destruct command followed by the code - which was One-Two-Three-Continuity. He would then repeat the abort auto-destruct command. At this point the computer would cancel the sequence.
For the refit Constitution class starships that was seen in the first six movies, the self-destruct sequence was basically the same. However in this instance, the sequence was sixty seconds long, rather than 30 seconds.
While not canon, the book Mr. Scott's Guide to the Enterprise explains the auto-destruct sequence in greater detail. In the book, the Enterprise is described as having two destruct systems. If the final code given was Zero-Zero-Zero-Destruct-One, the warp core would overload, and the ship would be destroyed in a sun-like antimatter fireball. This fireball would also consume any nearby object. In the event the ship was near a planet or another object to be preserved, the secondary destruct system was used. It would be activated if the final code was Zero-Zero-Zero-Destruct-Zero. In the event this destruct system was used, the ship would eject the antimatter. It would then overload all the electrical systems, and then detonate powerful charges located throughout the hull. By the time the sequence had completed, the ship would be a lifeless hulk which would be worthless to enemy forces.
On the Galaxy Class starship, the destruct sequence was started from main engineering. The Captain and First Officer would touch a panel on the master situation table. The computer would then recognize the two officers. The Captain would tell the computer to start the destruct sequence. The computer would ask the first officer if he agreed. If the First Officer gave his consent, the ship would begin a countdown. The time limit was flexible, the Captain had an option of specifying how long the ship should wait before destroying itself. But if no time limit was specified, the ship had a default of five minutes. The Captain could abort the auto-destruct sequence by telling the computer to do so. The computer would ask the First Officer if he agreeed, if he did so the destruct sequence would be canceled.
It has not been clearly documented whether or not it was a requirement that the officers gather in Engineering. The wisdom of making them go to engineering would be debatable if access to that part of the ship had been blocked.
The Star Trek: The Next Generation Technical Manual went into greater detail about the destruct sequences on Galaxy-class starships. On this type of vessel, the sequence could be aborted at any time before the sequence reached T -minus zero. Galaxy class ships also had two destruct devices. The first type involved the vessel's warp drive overloading, and the shut down of the anti-matter storage bottle containment fields. The vessel would vaporize due to explosive and thermel shock. It was estimated that such an explosion would be equivalent to 1,600 photon torpedoes. The second type was a backup if the first method failed, or if destruct was called for in the primary hull during separated flight operations. In this method, a number of charges located at key points throughout the ship were detonated. This had the equivalent of about 1,000 photon torpedoes. The system would check to see who was available on the ship, and would accept auto destruct commands down to the level of operations manager.
On Soverign class starship s, such as the USS Enterprise-E, the sequence is closer to what was given on Constitution class starships. the Captain would order the computer to begin the destruct sequence. The next two highest ranking officers who were present would give their assent. At that point the Captain would give the final clearance. He could specify a time limit, and whether or not there were to be any further announcements regarding the auto-destruct.