The Enterprise is summoned to a space station without explanation and told that the crew will be removed to the space station. Upon arriving, Kirk is contacted by Commodore Enright and told that Commodore Bob Wesley will be beaming aboard. Kirk finds out from Wesley that has been given the ``honor'' of testing of Dr. Daystrum's M5 Multitronic System, a computer designed to replace the crew of a starship. McCoy has misgivings about the test, but Kirk has no choice but to go along with it.
Spock is impressed with the device and believes it to be potentially even more important than Daystrom's advances in duotronics. However, Kirk learns that the device is called M5 because the first four generations were not entirely successful, leading him to have misgivings. Kirk does not believe that his misgivings are entirely due to his own jealousy that his job could be partially or completely replaced by a machine.
The M5 appears to function normally at first. When it is engaged to enter orbit around Alpha Carinae 2 and make recommendations for a landing party, Kirk is chagrined to find out that the M5's recommendations are the same as his own, with the exception that he and McCoy are not included since they are ``nonessential personnel.'' Meanwhile, M5 begins turning off power to unoccupied parts of the ship, at the same time drawing an increased amount of power.
In an unscheduled drill at Alpha Carinae 2, M5 defends the Enterprise against attacks from the starships Excalibur and Lexington, the latter which is commanded by Wesley. The M5 is declared the victor of the simulated contest, prompting Commodore Bob Wesley to call Kirk ``Captain Dunsel.'' Spock explains the meaning of ``dunsel'' to McCoy as a term used by midshipmen at the Federation Academy for a part which serves no useful purpose.
In a short time, however, M5 takes control of the Enterprise despite Kirk, Sulu, and Scott's attempts to regain control. It then locks phasers at full power and destroys the automated ore freighter Wotan when it passes nearby. When Kirk tries to disconnect the M5, he discovers that M5 has generated a protective force field which prevents any one from getting near it. Scott assigns a technician to unplug the connection, but he is immolated when he tries to disconnect it. M5 has conveniently picked the instant of the technician's action with the establishment of a direct link between itself and the connector so that it may draw power directly from the warp engines. Spock and Scott desperately attempt to manually override before a scheduled rendezvous with the exercise force. Daystrom is surprised by the M5's actions, but views its behavior as mistakes made by a ``child'' who is still learning.
Unfortunately, implementing manual override fails when M5 reroutes helm and navigation control using the H279 elements and rendering the G95 systems dead. When Daystrom is questioned about M5's irrational behavior, he reveals that he has impressed human engrams in the circuitry, providing a system nearly as complicated as human synapses. At the scheduled rendezvous point, the M5 attacks the Excalibur, Lexington, Hood, and Potemkin, killing many crew members (53 on theLexington and initially 12 on the Excalibur, including its Captain Harris and the first officer).
Daystrom now reveals that the engrams were his own, and Kirk and company surmise that M5 therefore suffers from the mental instability which Daystrom now reveals (as he rails on his colleagues for laughing behind his back and becoming successful by stealing and building on his work). Kirk finally shuts off M5 by pointing out that by killing humans it has violated its programming of saving men from dangerous activities such as space exploration. Since the penalty for murder is death, the M5 concludes that it must die, and shuts itself down. While preventing Kirk from regaining control, it also drops shields, leaving the Enterprise open to retaliatory attacks from the task force. However, when Wesley sees that the Enterprise has dropped its shields, he calls off the attack.
Dr. Daystrom is committed to a program of rehabilitation, but Spock still refuses to respond to McCoy's prodding that that human compassion outweighs any advantages computer may have in computational ability. McCoy further annoys Spock by suggesting that people are more pleasant to be around than computers.