As the Enterprise is on its way New Paris on Marcus III, it encounters a strange natural phenomenon. Commissioner Ferris wants Kirk to hurry on to New Paris, but Kirk is under orders to study all quasars and quasar-like phenomena and so stops the Enterprise in order to do so. Kirk launches the shuttlecraft Galileo (NCC 1701/7) with Spock, Scotty, McCoy, Boma, Latimer, Gaetano, and yeoman Mears aboard.
The 24-foot-long shuttlecraft is pulled off course into the Murasaki 312 electromagnetic storm (``Murasaki effect'') and crash lands on Taurus II. It and its crew are in one piece, but the shuttlecraft is greatly damaged. As Spock puts it, ``Picturesque descriptions will not mend broken circuits, Mr. Scott. I believe you have your work cut out for you.'' Taurus II seems safe at first (atmosphere 70 mmHg of oxygen, 140 mmHg nitrogen, and acceptable quantities of Ar, Ne, and Kr), so Spock sends Latimer and Gaetano outside to scout the area.
Meanwhile, Commissioner Ferris continues pressuring Kirk to leave the shuttle behind in order to get needed medicine to the plague victims in New Paris, but Kirk continues the search until the last possible moment. In an act of desperation, Kirk sends out shuttlecraft Columbus to search Taurus II (the only planet which is habitable in the area, and the one which is closest to the center of the Murasaki effect).
On Taurus II, Spock gets his first taste of command, much to the resentment of his crew. Spock sums up his views on command by stating, ``I neither enjoy the idea of command, nor am I frightened by it. It simply exists.'' Scott determines that much fuel has been lost and that the shuttlecraft's weight must be reduced by 500 lbs. if it is to achieve escape velocity. While scouting the area, Latimer and Gaetano enter a thick mist. They then hear a croaking noise and are shortly thereafter attacked by the planet's 10-12 foot high ape-like inhabitants. Latimer is killed by a spear whose tip resembles a Folsom point, but Spock's archeological knowledge just makes his crew more resentful.
Boma insists on a funeral for Latimer, but Spock remains inside the craft with Scott trying to fix it. Unfortunately, they lose the remaining fuel when a line breaks. The crew wants to attack the apes, but Spock does not which to unnecessarily take life, so he instructs them to fire to frighten, but not kill. Spock orders Boma back to help with repairs, while Gaetano is left behind. Alone and terrified, Gaetano has his phaser knocked away and is then mauled to death.
Scotty proposes powering the shuttlecraft by draining energy from phasers, which is all well and good, except that it is the crew's only remaining defense against the creatures. Spock goes to investigate what has become of Gaetano, and carries his body back despite a rain of spears from the ape-creatures. Arriving back safely, Spock is surprised that his logical decisions have resulted in two deaths and the antagonism of his crew. The crew retreats to the craft, which is then set upon by one of the apes with a large rock. Spock comes up with the idea of draining the batteries to electrify the exterior of the ship, which grants them a temporary respite. Unbeknownst to the crew of the Galileo, Kirk beams down landing parties, but they are unable to discover anything. Lt. Kelowitz from landing party 2 reports one dead, two injured by the anthropoid creatures, who databases classify as order 4AG and resembling creatures from Hanson's Planet. Ferris forces Kirk to abandon the search when his time runs out, under Title 15 of the Galactic Emergency Procedures.
Scotty manages to get the shuttlecraft off the ground after tarrying shortly to give Spock time to get on board after he is slightly injured. The Galileo's crew is saved when Spock jettisons and ignites the fuel to serve as a flare. This gives them only a few minutes before re-entering, but allows them to be seen by the Enterprise and transported to safety. Kirk needles Spock about his act of desperation, but Spock defends his actions logical considering that all other alternatives had been exhausted.