Kirk is leading a landing party which has discovered rich deposits of tritatium when he starts to notice a strangely familiar, sweet, honey-like smell in the air. He quickly sends three security men to search for dikironium, telling them that if they see a gaseous cloud they are to fire on it immediately. A reading is picked up by the men but vanishes, at which point the cloud attacks them. Only Rizzo survives, to be found by Kirk and Spock.

The Enterprise has orders to rendezvous with the U.S.S. Yorktown to collect a cargo of vaccine but, despite the perishable and urgent nature of the goods, Kirk refuses to leave until the cause of the deaths has been confirmed. McCoy is at a loss until Kirk tells him to check the medical logs of the U.S.S. Farragut which had the same experience eleven years earlier. On the bridge, Kirk tells Spock to search for an intelligent, gaseous creature that is able to conceal itself. Spock replies that it could only do so if it were able to change its molecular structure.

Another ex-Farragut crewman, Garrovick, who is the son of the Farragut's dead captain, reports to the bridge and is with Kirk when they hear that Rizzo has died in sickbay. Kirk and Garrovick join a security team that beams down to the planet and they soon find evidence that the creature can, indeed, change its molecular structure. Garrovick sights the creature and fires his phaser at it, to no effect. One security man is killed and another is in critical condition following the attack.

In debriefing, Garrovick admits to a momentary pause before opening fire which leads Kirk to relieve him of duties and confine him to quarters despite McCoy's observation that he is being too hard on him. Spock questions McCoy about the captain's apparently obsessive behaviour and is told by the doctor that Kirk, then a lieutenant, was one of the survivors of the previous encounter with the cloud in which half of the Farragut's crew, including Garrovick's father who was the captain, died. Kirk admits to McCoy that eleven years ago he, too, had hesitated before opening fire and feels responsible for what happened. McCoy accuses Kirk of being obsessed by the creature and summons Spock to help him consider Kirk's fitness for command.

Kirk explains that the creature is obviously intelligent and poses a major threat to inhabited planets, which temporarily satisfies them. Chekov detects the cloud creature moving away from the planet into space and Kirk orders the Enterprise to pursue it at maximum warp. The ship, however, cannot sustain the speed and is forced to drop to warp six. Amazingly, the cloud reduces its speed as well, dropping to warp two as if preparing for a confrontation and allowing them to catch up. Battle stations are sounded and Garrovick assumes his position on the bridge, watching as the Enterprise fires phasers and photon torpedoes at the creature, to no effect.

Spock informs Kirk that the deflector shields are also unlikely to stop the creature and this proves to be true when the creature approaches the ship and enters the ventilation system through an open impulse vent. The system has to be shut down, leaving them with only two hours air supply. Kirk orders Scotty to flood the system with radioactive waste. Spock is now convinced of the creature's intelligence and malevolent intentions. He speaks to Kirk and informs him that the creature can obviously shift itself in space and time, meaning that whatever Kirk had done eleven years ago would have had the same result and that there is no point in blaming himself for the outcome of his actions. He gives the same explanation to Garrovick but, while they are talking, the creature enters the room through an air vent.

Spock bundles Garrovick out and tries to close off the vent while Garrovick contacts the bridge. Kirk orders Scotty to reverse the room pressure, sucking the creature back into the ventilation system. The creature eventually leaves the Enterprise, heading for Tycho IV, which seems to be its home and where it attacked the crew of the Farragut. Kirk and Garrovick beam down to the surface with haemoplasm, hoping to attract the creature to them. Before they can make their planned use of it, the creature consumes it, so Kirk uses himself as bait. He and Garrovick stand next to an antimatter device they have brought with them, luring the creature closer. At the last moment they beam up to the ship and the antimatter is detonated, destroying the creature. As the Enterprise resumes its course for rendezvous with the Yorktown, Kirk takes Garrovick to one side and promises to tell him a few stories about his father.