At the planet Argo, a team from the Enterprise takes an aquashuttle to the surface. The planet is almost completely covered in water due to earthquakes and other seismic phenomena, and the Enterprise needs to study the effects since another Federation world will soon go through the same planetary changes. Unfortunately, the shuttle is attacked by a giant sur-snake, and Captain Kirk and Mr. Spock are taken away.
When a search party finds the two officers five days later, they discover that the men have been mutated by an unknown hormone: their hands are webbed, their eyes have a second lid, and they breathe water now instead of air! Despite his best efforts, Dr. McCoy is unable to revert them to their original physiology. Kirk and Spock return to the waters of Argo to investigate, whereupon they are captured by the sentient race of Aquans. Fearing the once-airbreathers mean them harm, the Aquan Ruling Tribunal sentences them to die on an unsunken landmass.
An Aquan girl named Rila helps an Enterprise rescue party to find and rescue Kirk and Spock, but they have horrible news: ship's sensors indicate a new seaquake will wipe out the Aquan underwater city within two hours! Rila also informs them that there are hidden records in sunken ruins of how to reverse the mutation that changed Kirk and Spock. The pair find the records, and after a close call with a sur-snake, return with them to the Enterprise.
Learning that the venom of the sur-snake is the key to reversing their mutations, Kirk and Spock are aided by Rila and several others to gain some of the venom, Through trial and error, McCoy is able to use the venom to revert the officers back to human. The Enterprise then uses its phasers to bombard the unpopulated areas of the seabed, thus changing the epicenter of the massive sea quakes. Their city saved, the Aquans are grateful to Kirk and his crew, and vow to allow the younger Aquans to explore life on the remaining surface land-masses if they choose to do so.