The Federation starship USS Enterprise receives a scrambled message from Starfleet about the USS Intrepid, a Federation vessel crewed entirely by Vulcans. Spock suddenly appears shocked, announcing that he felt the Intrepid "die." Nevertheless, Starfleet successfully contacts them, ordering Captain Kirk to investigate the Gamma 7A system, the Intrepid's last known position. Chekov reports no life readings in the design, which had a billion inhabitants.

Spock returns to the bridge as Uhura loses contact with Starfleet. Kirk orders Spock to scan a dark zone on the main view screen, causing half the crew to feel sick or faint. Spock cannot identify the zone but suggests it might be energy turbulence, possibly responsible for the deaths of the system's inhabitants and the Intrepid crew. Kirk orders a sensor probe to be launched into the void, which transmits a high-pitched noise before losing contact.

Kirk orders the ship into the zone, causing the piercing sound to return and stars to disappear from the main view screen. McCoy reports worsening crew conditions, and Scott reports power loss. Spock theorizes that they have entered a negative energy field that interferes with biological and mechanical processes.

The Enterprise accelerates involuntarily, and its engines seem to operate in reverse. Kirk suggests channeling all power into a massive forward thrust to escape the zone, but it only brings the ship to a halt.

A gigantic, multicolored amoeba-like object is revealed. Kirk launches a sensor probe, discovering the object is made of protoplasm and alive. McCoy believes a crewed probe must gather data to destroy it, volunteering himself. Spock insists he is better qualified, and Kirk ultimately chooses him. Spock pilots a shuttle through the creature's outer membrane toward the nucleus, reporting it is about to reproduce. He suggests a method to destroy it, but the critical part of the message is garbled. Kirk and McCoy discuss the situation, and Kirk speculates that "antibodies" are needed to destroy it.

Kirk takes the Enterprise into the creature's body and orders Scott to prepare an antimatter bomb with a seven-minute timer. The bomb is fired into the cell's nucleus, and the Enterprise backs out using its remaining power. With seconds left, Spock's shuttle is located and towed by a tractor beam. As power levels are nearly depleted, the ship approaches the outer membrane just as the bomb explodes. The Enterprise and the shuttle are thrown clear of the organism as it is destroyed. Nevertheless, the Enterprise regains full power and sustains minor damage.