Stardate 4307.1: The Enterprise is heading for Starbase 6 for R&R when Uhura gets a report about their sister ship the Intrepid, an all-Vulcan starship. Spock suddenly reacts in pain then informs Kirk and McCoy that the Intrepid… died, and every Vulcan aboard died with it. McCoy takes Spock to sickbay while Uhura gets a clear transmission with orders to divert to investigate the Intrepid's disappearance in a solar system. Chekov manning the science station reports that the entire solar system is… dead.
In sickbay, Spock explains that even he could hear the death-screams of 400+ Vulcans. Back on the bridge they approach the area of the missing star system and spot a large black impenetrable object. They launch a probe and the feedback nearly deafens them and then Uhura displays signs of weakness. McCoy reports that other crewmen are reporting similar signs of fatigue and he's issuing stimulants. Spock is unable to provide any information on what they are observing and can only eliminate the possibilities of what they know it isn't. Kirk orders them into the area of darkness with deflectors at full. Another burst of feedback overwhelms the ship directly and then fades away, and they can see nothing outside the ship. The crew are weakening and Scotty reports they've lost 5% of their power reserves and they can't compensate of the drain continues. As McCoy gives out stimulants, Spock reports they are in an area inimical to human life and McCoy confirms that they are all dying.
The Enterprise stops within the zone of darkness and when Scotty recalibrates the engines, the ship lurches forward when the chief engineer tries to reverse the engines. The energy drain on the engines continues and Spock reports they are being pulled toward the center of the zone. Spock quickly concludes that their energy is reversed and they engage forward thrust, which works to slow them although the energy drains. Spock concludes the zone of darkness is a negative energy force but not the source of the drain. Kirk orders Scotty to put all their energy into one forward thrust and although the ship is rattled, they aren't able to get free and can barely hold their position. Scotty warns they have only two hours until the engines are drained. Spock points out that they've found the center of the zone: a glowing amoeba shape. They launch a probe into it and discover it's 11,000 miles long and 2-3,000 miles wide, with an interior of protoplasm. The "creature" is a living being… and it is drawing the ship in to its death.
McCoy analyzes the creature and concludes they are facing a one-celled organism. He and Spock both suggest they send a one-man shuttlecraft in to get necessary information and McCoy and Spock via for the mission, while pointing out that Kirk can't go. Kirk eventually agrees to consider it.
Later Kirk calls Spock and McCoy to his quarters as Scotty reports they are down to 50% power reserves. Kirk orders him to prepare the shuttlecraft for launch and then apologizes to Spock… for having to pick him as the best-qualified to go. McCoy bids Spock farewell… and wishes him luck once he's out of earshot.
Spock takes the shuttlecraft toward the creature's core and diverts energy to shields, although it won't leave him enough power to get out. Spock penetrates the creatures outer skin, rattling both vessels, then manages to reestablish contact. He heads toward the nucleus while reducing his life support to minimum, then reports that it has stored enough energy to reproduce. They lose voice contact but Spock is able to transmit the coordinates of the chromosome bodies. Spock then manages to stimulate it enough to signal that he's still alive and they determine if the creature reproduces it will continue to do so until it encompasses the entire galaxy. The energy drain on the Enterprise is critical and Spock manages to send a message saying the creature is vulnerable from within but is cut off before he can send the means.
Kirk and McCoy discuss how they are acting as antibodies against the invading amoeba/virus, and Kirk figures out they should use anti-matter. He tells Scotty to divert all energy except impulse to shields, causing them to be sucked in. They successfully enter the nucleus and Kirk orders an anti-matter charge prepared. However they have to get as close to the chromosomes as possible.
Spock prepares a final log entry, entering his commendations for the crew. Kirk does the same and then they launch the anti-matter probe into the nucleus. With seven minutes left, they start to back out and locate Spock. They put two tractor beams on him despite the energy drain and get to the membrane… just as the power levels go dead. The anti-matter pod explodes and the Enterprise is blasted free as the organism is destroyed. They maintained a lock on the shuttlecraft and Spock requests permission to come aboard. They bring Spock aboard and head to the starbase for some rest and relaxation.