When Spock is stricken down by a disease fatal to Vulcans, the Enterprise is to meet a freighter with a load of drugs that provides the only cure, but Orion pirates attack the ship and Kirk must track down the Orions and the drug before it is too late.
The Enterprise has as an observer on their current exploration/contact missions: Commander Ari bn Bem of the planet Pandro. He is rude and obnoxious and dangerously independent, but Kirk is under orders to treat him well to further relations with Pandro. After six months in his cabin Bem insists on going on a landing party. Trying to rescue Bem (who claims he is observing the primitive locals), Kirk and Spock are captured. Bem has replaced their communicators and phasers with dummies to observe them under stress as well. He reveals he is a colony creature who can split his body into separate, individually independent parts. Meanwhile, a sensory anomaly is sweeping over the planet, and appears to be a ""god"" of some sort that claims responsibility over its ""children"" and insists they leave. Bem escapes and Kirk rescues him again by telling the ""god"" that he has the same responsibility to Bem it does to her children. A chastened Bem acquiesces and the planet's natives are left to develop
The Enterprise explores a mysterious cloud in space. After passing through it the ship's computer begins acting in a bizarre fashion. It replicates Kirk's shirts with ""Kirk is a Jerk"" on the back, manufacturers devices that leave a black eye ring on Spock, and shoot cream pies out of the food devices. Things take a turn for the worse when McCoy, Sulu, and Uhura are trapped in thea holodeck where they are beset by dangerous weather phenomena. They are rescued by Scotty when he bypasses the controls, but the Enterprise crew are further endangered when the Romulans attack and the ship's computer overrides manual controls. By feigning fear of the cloud, Kirk tricks the ship's computer into entering the cloud, which reverses the process. As they depart, they pick up transmissions from the pursuing Romulan ship that they are experiencing strange phenomena from their computer...
Dr. McCoy is arrested and held responsible for causing a plague that ravaged the planet Dramia Two, where he performed a mass-innoculation 19 years earlier.
The Enterprise is tracing the course of a probe that scanned Earth and sent a signal back along its course. They are attacked by a serpent-shaped energy field belonging to a feathered serpent who claims to be Kulkukan of Mayan-Aztec legend. It beams Kirk, McCoy, Scott, and Ensign Walking Bear aboard its ship to solve its puzzle before he will reveal himself. Aligning the mirrors in a strange city, they solve the puzzle and Kulkukan appears before them. It takes them to its ""zoo"" of violent creatures that now live in tranquility. Spock figures a way to break Kulkukan's force field and Kirk uses the diversion to free the animals. Kulkukan realizes that is not a god, but just a delusional old alien that once helped the younger races along. It leaves in sadness, leaving McCoy to remember the Shakespearean quote, ""How sharper than a serpent's tooth is an ungrateful child...""
With Commodore Robert April (the first commander of the Enterprise) on board, Kirk pursues a ship plunging into a supernova, and enters a universe where time runs backwards.
