While the USS Enterprise was circling a strange planet causing temporal distortions, the Chief Medical Officer, Dr. Leonard McCoy, was attending to a wounded Lieutenant Sulu when another temporal wave hit the Enterprise, and McCoy mistakenly injected himself with an overdose of hydrazine, a toxic drug. As a result, he became delirious and anxious, exiting the bridge and materializing himself on the planet. Captain James T. Kirk then enlisted a search party of his first officer, Mr. Spock, the chief engineer, Mr. Scott, and the communications officer, Lieutenant Uhura, to go and look for him. Once they reached the surface, they found a radiant, intelligent archway known as the "Guardian of Forever," an entrance that could transport them to any era and location.

The Guardian allows them to return to Earth's past and then presents a selection of visuals from historical eras, which Spock records with his tricorder for further analysis. As the rest are occupied, the mentally unstable Dr. McCoy reveals himself from his concealment and leaps through the portal. In an instant, the away team loses communication with the Enterprise. The Guardian clarifies that McCoy has changed the past to such a degree that the Enterprise and their former reality no longer exist.

According to The Guardian, it is possible to reverse the damage done. This prompts Kirk to ask for a replay of the period that was showing when McCoy went through. He and Spock then attempt to time-travel to a moment just before McCoy's emergence and find themselves in New York City during the Great Depression. To blend in, they swipe some clothes from a fire escape, and while trying to avoid being apprehended by a policeman, they take refuge in the basement of 21st Street Mission. There, they meet Edith Keeler, who oversees the soup kitchen. She notices something peculiar about the two visitors, yet still offers them money to clean up the basement and finds them a place to live. Spock then tries to figure out how McCoy altered history by using his tricorder to access the recordings.

Spock highlights how complex the job is using the outdated technology of 1930, which he compares to primitive tools. As Spock grapples with the engineering issue, Kirk finds a job at the 21st Street Mission to cover their expenses and meets Edith Keeler, whom he adores.

Unbeknownst to Kirk and Spock, McCoy finally turns up very disturbed and collapses during the mission, where Keeler nurses him back to health. Spock completes his work and discovers that Keeler was supposed to die in a car accident but was saved by McCoy's presence, resulting in a changed timeline in which she created a peace-loving movement on the brink of World War II. This causes the US to put off joining the war, allowing Nazi Germany to construct the first atomic bomb and take advantage of it to take control of the world. Kirk is deeply disturbed by this revelation and confesses his love for Keeler, to which Spock responds that she must die to stop numerous deaths and restore the future.

While walking to a movie with Kirk the following evening, Keeler casually, When going out to watch a film with Kirk the next night, Keeler brings up McCoy's passing. Startled, Kirk tells her to remain where she is while he rushes off to inform Spock of the news. McCoy occurs to come out of the mission at the same time, and the trio reunites on the sidewalk. Seeing this, Keeler starts to cross the street to be with them and doesn't notice an oncoming truck. Kirk automatically turns to protect her, but a shout from Spock causes him to stay still, and Kirk pulls McCoy back so he can't save her either. Keeler is struck by the truck and killed, and an astonished McCoy asks Kirk if he knows what he just did. "He is aware, doctor," Spock answers, "He is aware."

After their time travel, Kirk, Spock, and McCoy returned to their companions through the Guardian. The astonished Mr. Scott describes that only a brief moment had passed for the others, though Spock and Kirk had been gone for several weeks. Kirk refuses to answer questions about his experience, and upon hearing the Guardian's remark that "many such journeys are possible," he remarks, "Let's get the hell out of here." The team is transported to the Enterprise.