The USS Enterprise, investigating a series of mysteriously devastated star systems, intercepts an automated distress signal from its sister ship, the USS Constellation. Upon arrival, they find the Constellation severely damaged and adrift in space. Captain Kirk, Dr. McCoy, Chief Engineer Scott, and a damage control team were transported to the ship to assess the situation. They discover Commodore Matt Decker, the ship's commander, as the sole crew member remaining onboard, suffering from extreme mental shock.

After receiving a sedative from Dr. McCoy, Decker reveals that he and his crew had encountered a massive machine, miles long, that used antiproton beams to disintegrate planets and consume the debris for fuel. The Constellation's attack on the machine was unsuccessful, resulting in significant damage to the ship. Decker evacuated his crew to one of the planets in the system, only for the machine to destroy it. Kirk hypothesizes that the machine is an ancient doomsday device and must be stopped before reaching more populated areas of the galaxy. McCoy and Decker transport to the Enterprise, which has taken the Constellation in tow, while Scott's damage control team attempts repairs on Constellation's damaged impulse engines, weapons, and shields. Kirk works on the nonfunctional viewscreen of the Constellation, which will be his only means of monitoring external events aside from communications from the Enterprise.

Spock, the first officer of the Enterprise, alerts Kirk to the unexpected appearance of the so-called planet killer, which starts pursuing the Enterprise. As the boarding party prepares to return, the machine attacks the Enterprise, damaging the transporter and disrupting communications. Being the highest-ranking officer on the Enterprise, Decker takes command and orders a phaser attack. However, the phasers do not affect the machine due to its solid neutronium hull, and the ship gets trapped in a tractor beam, pulling it toward the planet killer's mouth.

Kirk successfully repairs Constellation's viewscreen and is stunned to see the Enterprise engaging with the machine. Scott manages to fix the impulse engines and recharge one of Constellation's phaser banks. Kirk uses the impaired ship to approach and fire at the planet killer, distracting it long enough for the Enterprise to break free from the tractor beam. After fixing the transporter and reestablishing voice communication, the Enterprise retreats to a safe distance. Per Kirk's orders, Spock relieves Decker of command, and Decker is escorted to Sickbay.

Nonetheless, Decker overpowers his security escort and commandeers a shuttlecraft. Consumed by guilt over his crew's loss, Decker informs Spock that he intends to fly the shuttlecraft directly into the machine's maw. Despite Kirk's plea for him to return to the Enterprise, Decker remains committed to his course and ultimately perishes.

Lt. Sulu observes a minor decrease in the planet killer's energy output following the shuttlecraft explosion. Kirk realizes this might have been Decker's intention and theorizes that a starship could cause more significant damage. Despite Spock's objections, Kirk decides to pilot the damaged Constellation himself. Scott sets up the impulse engines to explode with a thirty-second delay, cautioning Kirk that the detonation cannot be stopped once initiated.

After the boarding party is transported back to the Enterprise, Kirk aims the Constellation at the planet killer's mouth, activates the timer, and requests to be beamed back to the Enterprise—the transporter malfunctions, prompting Scott to work frantically to fix it with guidance from Spock. With barely any time left, Kirk is safely transported to the Enterprise just as the Constellation explodes within the planet killer, destroying its power system and rendering it inert in space, thus ending the threat. However, Kirk and Spock contemplate the possibility of more doomsday machines existing elsewhere.