The Federation starship Enterprise is summoned to a space station without explanation. Commodore Wesley (Barry Russo) explains that the Enterprise will be a test vessel for the M-5 Multitronic System, a revolutionary tactical and control computer designed by Dr. Richard Daystrom (William Marshall). The M-5 is to handle all ship functions without human assistance. While Science Officer Spock is impressed with M-5, Captain Kirk and Chief Medical Officer Dr. McCoy have doubts.

The M-5 succeeds at its first tasks, performing ship functions more quickly and efficiently than a living crew. However, M-5 also exhibits unexpected behavior, such as turning off power and life support to unoccupied parts of the ship and drawing increased power for unknown reasons; Daystrom maintains M-5 is working correctly.

M-5 defends the Enterprise against mock attacks from Starships Excalibur and Lexington in its first tactical drill. The Enterprise is declared the victor. Wesley jokingly refers to Kirk as "Captain Dunsel," employing a Starfleet Academy slang term for a part serving no useful purpose. Kirk is troubled by this.

Sometime later, M-5 detects the unmanned freighter Woden and attacks with live torpedoes, destroying it. Kirk orders M-5 taken offline but, on attempting to do so, finds it protected by a powerful force field. Chief Engineer Scott orders Ensign Harper to disconnect its power source. Still, the M-5 directly connects to the ship's warp engines, vaporizing Harper. Spock and Scott attempt a manual override but discover that the M-5 has rerouted all controls. Spock questions Daystrom on his computer design, and Daystrom reveals that he has imprinted human engrams onto M-5's circuits, creating what amounts to a human mind operating at the speed of a computer.

Meanwhile, four of Enterprise's sister ships, Lexington, Potemkin, Excalibur, and Hood, approach to begin a new tactical drill. Since M-5 has disabled communications, Kirk cannot warn M-5's targets. Nevertheless, M-5 detects the ships and attacks them with full-strength weapons. The crew watches helplessly as the Enterprise fires on the Lexington, killing 53, then turns to the Excalibur, killing all aboard and leaving her adrift. Commodore Wesley assumes Kirk is responsible for the attacks and requests permission from Starfleet Command to destroy the Enterprise.

Daystrom, having indicated that the engrams he used were his own, believes he can reason with the M-5, but his conversation with the unit quickly degenerates into a self-pitying lament over his own career disappointments. McCoy warns Kirk that he sees a psychotic episode coming. As Daystrom loudly proclaims his and his creation's invincibility, Spock subdues him with a Vulcan nerve pinch.

Kirk then tries to persuade the M-5 to stop its attacks. The M-5 acknowledges Kirk, who asks M-5 what its purpose is. M-5 responds that its purpose is to protect lives. Kirk rejoins that it acted contrary to its purpose by murdering people. M-5 acknowledges that it has committed murder and must therefore die and shuts itself down. In so doing, it also cripples the Enterprise.

Having received permission to destroy Enterprise, the other Federation ships close in. Since Scott cannot restore communications immediately, Kirk decides to allow the ship to drift with shields down, hoping that Commodore Wesley will realize that the threat has passed. The gamble pays off as the Commodore orders his ships to stand down at the last moment.