After beaming down to a planet to examine tritantium deposits (21.4 times as hard as diamond), Kirk notices a sweet, honey-like odor. He recognizes it as something he encountered 11 years ago, and orders the security guards to scan for choronium and fire at any gaseous cloud they encounter. Two security guards are killed by the gaseous creature after it removes the red corpuscles and feeds on their hemoglobin. Kirk, Spock, and Ensign Rizzo survive, but Rizzo has much of his hemoglobin removed and must be beamed back to the Enterprise for treatment.
Kirk becomes obsessed with the destruction of the creature, which killed half the crew of the U.S.S. Farragut (including its commander Captain Garrovick), Kirk's first deep-space assignment. Kirk appears to willing to miss his rendezvous with the U.S.S. Yorktown, the ship he is supposed to rendezvous with in order to deliver perishable vaccines for the planet Theta 7.
After Rizzo dies, Kirk beams back down with a landing party which includes Ensign Garrovick (Captain Garrovick's son). Garrovick fires phaser 2 when he spots the gas cloud, but not before two other officers have been attacked. Kirk grills Garrovick, accuses him of ``freezing up'' and being responsible for the death of one officer and severe injury of the other, then relives him of duty.
Reading the log file of the Farragut incident, Spock learns that Kirk's obsession is fueled by the fact that he was the one who ``froze'' 11 years previously, and has been blaming himself for the deaths of half the ship's crew members even since. When Chekov detects the creature leaving the planet's surface and heading into space, Kirk pursues it.
Scanners report that the creature is in a border state between matter and energy. The creature slows and then heads for the Enterprise. Neither phasers nor photon torpedoes damage it, and it enters the ship through the number 2 impulse vent which had inadvertently been left open by Scott after performing maintenance. Spock realizes that the reason for the creature's immunity to weapons fire is because it is able to move itself in time to avoid phaser fire.
On board the Enterprise, the creature attacks two crew men, and entered the ventilation system. Spock goes to explain the creature's ability to avoid being hit by phasers to Garrovick, but is then attacked by it when he tries to prevent it from entering Garrovick's room though the ventilation shaft. Spock is saved only become his hemoglobin is based on copper. (McCoy: ``That green blood of his... left a bad taste in the creature's mouth.'' Spock: ``Colloquially expressed, but essentially correct.'')
The creature then leaves the ship and heads away at warp speed, but Kirk has a hunch of where the creature is headed. In some mystical way, Kirk has sensed that the ``home'' of the creature is planet 4 of the Tycho system, the location where the Farragut was attacked. Spock is in favor of the chase since his sensor readings indicate that the creature is about to fission into multiple copies.
Kirk and Garrovick beam down to the planet and set some hemoplasm as bait, but the creature takes the bait before the explosive charge of antimatter is ready. Kirk proposes to use himself as bait and orders Garrovick back to the ship. Garrovick attempts to knock him out and act as bait himself, but Kirk overpowers him. The two are then beamed up in the knick of time and the charge of antimatter is set off. After some difficulties with the transporter, Garrovick and Kirk arrive back on board the Enterprise safe and sound.