The Enterprise, heading to Starbase 6 for shore leave, intercepts a badly distorted message from Starfleet. Uhura can only make out the words 'U.S.S. Intrepid', which is crewed by Vulcans, and some co-ordinates. Spock shudders and doubles up in pain, following which he reports that the Intrepid has just 'died'. The Enterprise follows the heading given to sector 39j. No contact can be made with the Intrepid or with system Gamma 7A, which it was sent to investigate. Chekov reports that sensors indicate no life readings in the system despite its billions of inhabitants.

In sickbay, Spock explains to McCoy how he felt, in his mind, the shock and disbelief of the 400-strong Vulcan crew of the U.S.S. Intrepid as they died, despite the distances involved. He returns to the bridge to find that contact has been lost with Starfleet and a strange dark area of space is being displayed on the main view screen. Sensors indicate some sort of energy turbulence ahead and a probe is launched to investigate. Moments later a high-pitched noise is heard throughout the ship, that causes a large proportion of the crew to faint or feel ill.

The Enterprise holds position relative to the phenomenon while more data is gathered. It proves to be inconclusive so Kirk decides to get a little closer. As it approaches the phenomenon the high-pitched noise is heard again. When it stops, the stars have vanished from the main view screen. McCoy busies himself issuing stimulants to counteract the effects of the noise. He eventually contacts Kirk, telling him that his medical scanners indicate that the crew is slowly dying. Spock surmises that they have passed through a boundary layer into a region that is incompatible with their engineering and life forces and that energy is being slowly drained away from everything.

Kirk orders the ship into reverse but it moves forward instead. When forward thrust is applied, the ship slows down again. Scotty has been tinkering with the engines and the Enterprise makes one massive effort to get free of the negative energy field but does not have enough power. However, the massive amounts of energy expended in the attempt have attracted what appears to be an amoeba-like creature towards the ship and Spock confirms that it is the source of the energy drain. A probe is launched in its direction, the telemetry recovered indicating that the creature is protoplasmic in nature and, unbelievably, almost 11,000 miles long. McCoy believes that it is a simple single-cell organism that feeds on energy, but needs more data to confirm its true nature.

Spock persuades Kirk to allow him to take a shuttlecraft to examine it at close quarters, even though the mission appears to be suicidal. Shortly after launch, the shuttlecraft penetrates the surface of the creature and Spock starts navigating towards the nucleus. His life support systems are reduced to a bare minimum to conserve power and he continues to transmit data that indicates to McCoy that the creature is on the verge of reproducing. The final message received from Spock before his signal breaks up indicates that he believes the creature can be destroyed from inside, but the details are lost.

Kirk follows the shuttlecraft in the Enterprise, entering the creature and heading for the nucleus. He orders Scotty to prepare an anti-matter 'bomb' with a timer set for a seven minute delay. The charge is lodged in the creature's nucleus and their remaining power is used in getting away from the impending explosion but even on full impulse they only have seconds to spare. Suddenly, Spock's shuttlecraft is located and Kirk orders it to be towed with tractor beams even though it means losing precious time. As their power levels drop to zero the anti-matter 'bomb' explodes, destroying the creature and throwing both the Enterprise and the shuttlecraft back into normal space where Spock is retrieved safely, surviving only by virtue of his Vulcan metabolic control.