The USS Enterprise is on a daring journey to explore beyond the galaxy. Along the way, they come across the recorder of the SS Valiant, a lost Earth spacecraft that went missing 200 years ago. The recording was fragmentary, but it showed that the Valiant had been swept off-course by a "magnetic space storm" and that the crew had urgently looked up information on extrasensory perception (ESP) in the ship's computer. The last part of the recording showed the captain of the Valiant giving the order to self-destruct.

Captain Kirk resolved that they had to find out exactly what had happened to the Valiant, so the Enterprise set off across the edge of the galaxy. There, they ran into an odd wall that had a negative result on the ship's systems and warp drive, leaving them no option but to turn around. Nine crew members passed away, and helmsman Gary Mitchell and the vessel's psychiatrist Dr. Elizabeth Dehner (Sally Kellerman), were knocked out by the wall's influence. But when Mitchell woke up, his eyes shone an ethereal silver, and he was displaying incredible psychic abilities.

Mitchell's behavior towards the others grows more haughty and aggressive as he claims he has acquired divine-like abilities, highlighting his mental and physical powers. Spock surmises that the crew of the Valiant may have been subjected to the same phenomenon and destroyed their vessel to prevent its propagation. He suggests that Mitchell might have to be eliminated before his strengths become more formidable. However, Kirk adamantly denies this idea.

Worried that Mitchell would seize control of the Enterprise, Kirk determined to abandon him in the isolated world of Delta Vega, where a fully automated lithium-splitting station is located. After arriving, the team attempted to restrain Mitchell, but his strength was too strong. So instead, he used telekinesis to strangle navigator Lee Kelso and escaped by knocking out Kirk and Spock, taking along Dr. Dehner, who has now developed her psychic abilities.

Kirk implored Dr. Dehner's compassion to help him, but before he could, she used her supernatural abilities to debilitate Mitchell. Nonetheless, Mitchell gravely injured Dehner, yet before he could regain strength, Kirk fired his phaser rifle to cause a rockslide, resulting in Mitchell's death.

Back on the Enterprise, Kirk documented in the log that both Dehner and Mitchell had sacrificed their lives "in the line of duty." He told Spock he wanted his friend's personal record to end on a high note: "He didn't deserve this."