Spock is stricken ill with a disease that is fatal to Vulcans. With time running out, the Enterprise must rendezvous with another ship carrying the cure. However, Orion pirates hijack the shipment and Kirk must deal with them before Spock dies.
The Enterprise plays host to Ambassador Bem, an arrogant member of a neutral race. However, Bem endangers all of their lives when he conducts a test of suitability upon Kirk and Spock during an exploratory mission on a primitive planet.
After avoiding a Romulan ambush by entering a strange energy cloud, the Enterprise finds itself at the mercy of an insane ship's computer that indulges in a series of increasingly aggressive practical jokes.
The Enterprise goes to the planet Dramia II to deliver medical supplies, only to have McCoy arrested and put on trial for deliberately spreading a disease that wiped out an entire colony. Now Kirk must clear his friend's name before the doctor is executed.
Backtracking a mysterious probe, the Enterprise confronts a ship in the form of a giant feathered serpent. Its captain, Kukulkan, insists on putting Kirk and others through a test to determine if they have grown sufficiently to receive his wisdom.
The Enterprise inadvertently locks a tractor beam on a ship diving into a nova, and finds itself pulled into a bizarre parallel universe where time flies backward and the crew becomes younger at an alarming rate.