Captain Kirk, acting tense and irrational, orders the Enterprise straight into the Neutral Zone for no reason. Romulan warships (identical to Klingon ships due to sharing of technology) capture the Enterprise, and Kirk and Spock beam aboard the Romulan flagship.
When a landing party investigating Scalos begins to vanish one by one, Kirk, Spock and McCoy try to find out what is happening before more of the crew disappears, until Kirk himself is abducted. Kirk finds the cause to be a group of endangered Scalosians who move faster than human sight or hearing can detect. They need to repopulate their species, and find that speeding human males up to Scalosian speed will meet their needs.
Kirk, Spock and McCoy search for two missing scientists on a planet whose sun is about to explode, but they only find visual logs that show the scientists disappearing. Then the landing party disappears as well, finding themselves trapped by two aliens who snatched the scientists away and experimented on them until they died.
The Enterprise is carrying a new drug to the mental hospital on Elba II, where it is hoped that the last dangerously insane patients in the Federation can finally be treated. But when Kirk and Spock beam down, they do not realize that the facilities have been taken over by the inmates, led by Garth, a former Starfleet captain who has also become a shape-shifter.
Two natives of the planet Cheron are brought aboard after one of them helps the Enterprise chase the other down after he had stolen a shuttlecraft from a Federation starbase. Bele and Lokai, however, have a dispute that goes far beyond a simple pursuit of a criminal.
Kirk is planning to beam down to the overpopulated planet Gideon to meet with the leaders, but apparently arrives at the wrong place in a transporter malfunction (or so it seems to the Enterprise crew.) Kirk finds himself aboard the Enterprise, but cannot locate anyone else aboard except for Odona, who offers no answers to his bafflement at why no one is aboard the ship but him (or so he thinks).