The USS Enterprise, commanded by Captain Kirk, is on its way to Markus III to deliver medical supplies for the New Paris Colony when it encounters a quasar-like formation called Murasaki 312. Kirk's standing orders require him to investigate, so he dispatches a science team, including Spock, Dr. McCoy, Scott, Yeoman Mears, and three specialists (Latimer, Gaetano, and Boma), on the shuttlecraft Galileo. Unfortunately, the shuttle is pulled off course, forcing an emergency landing on the rocky, foggy planet Taurus II.

Latimer and Gaetano explore the area and encounter giant ape-like creatures wielding massive spears and shields. Latimer is killed, and Gaetano fends them off with phaser fire. The crew retreats to the Galileo, discovering that the creatures seem to be planning a coordinated attack. Spock decides to scare them away rather than kill them, resulting in Gaetano's death.

As Kirk searches for the shuttle, Commissioner Ferris pressures him to proceed to Markus III. Hindered by sensor interference, the shuttlecraft Columbus is sent to search from orbit, and search parties are beamed to the surface. One party reports encounters with the large furry creatures.

Amid attacks and internal disputes, the crew works to repair the shuttle. Scott adapts phasers to power the ship, but Boma insists on a proper burial for Gaetano and Latimer. Spock reluctantly agrees, and during the ceremony, the creatures attack again. A boulder pins Spock, but McCoy and Boma help him. Spock then lifts the Galileo using the shuttle's boosters, but with insufficient fuel to escape the planet or achieve a stable orbit. Spock dumps and ignites the remaining fuel in a last-ditch effort, creating a flare visible to the departing Enterprise. Kirk turns back, and the survivors are beamed out just as the shuttle is destroyed on re-entry.

Onboard the Enterprise, and Kirk questions Spock about his emotional motivations for the final action. Spock denies it but admits to stubbornness, causing the crew to laugh.