Kirk and Spock transport to the planet Organia, a pastoral realm of very low technology, which has the misfortune of being strategically important to the Klingons, who plan to use Organia as a forward base when they war on the Federation. Despite Kirk's best efforts, he cannot seem to impress upon the Organians that they are in dire peril and should ally with the Federation. Then the Klingons arrive, and being imposing martial law, and taking and executing hostages. Kirk works behind the scenes to interfere, but when the Organians betray him to the Klingons, he starts to wonder if they are worth protecting.

Ripples in time have provoked the curiosity of the Enterprise crew. One such ripple shakes the ship and gravely injures Sulu. McCoy brings him back from the brink with a powerful drug, but another ripple results in a tragic overdose, afflicting McCoy with dangerous paranoia! He beams down to the planet - the transporter was locked onto the source of the time disturbances. On the surface, he evades the landing party long enough to flee - into the past, where his psychosis results in him somehow erasing the Federation, and the Enterprise, save only the landing party. Their one chance is to use the same artifact - the self-styled Guardian of Forever - to arrive before McCoy and prevent him from changing their history.