A series of devastating quakes have left the planet Argo totally covered in water. The Enterprise journeys there to gather information that may help another Federation planet facing the same fate. The landing party, consisting of Kirk, Spock, McCoy and Lieutenant Clayton piloting the Aqua-Shuttle, are attacked by a giant sea monster called a sur-snake. McCoy and Clayton escape back to the ship, but Kirk and Spock are dragged underwater in the Aqua-Shuttle by the sur-snake.
Days later, the two are found near the wreckage of the Aqua-shuttle. They are uable to breathe, having been transformed in water breathers. Kirk and Spock beam back down to the planet to find the people who did this to them. Eventually, they discover an undersea race of intelligent beings who call themselves the Aquons. The Aquons are suspicious of the outsiders, thinking them spies from their air breathing enemies, and refuse to help them reverse their mutations.
Some of the younger Aquons defy the "ordainments" of the older Aquon Tribunes and lead the Enterprise officers to ancient ruins where they find old scrolls containing the cure for their condition. With another massive quake about to hit the area of the Aquon city, Kirk, Spock and the young Aquons race against time to gather the venom of a sur-snake for the antidote.
After Kirk and Spock are changed back to normal, Kirk uses the Enterprise's phasers to shift the epicenter of the coming quake away from the Aquon's city, saving their civilization. In gratitude, the Aquons vow to allow the Federation access to the ancient knowledge in the old ruins.
"The Ambergris Element," despite a somewhat ridiculous premise that stretches the suspension of disbelief almost to its limits, is actually surprisingly good episode. Its basically a generation gap fable, a popular theme for the time the episode was produced, with the young Aquons finding the courage to challenge the preconceptions of the older generation and help the outsiders. Of the five episodes, three for the original series and two for the animated revival, that Margaret Arman wrote for Star Trek, "The Ambergris Element" is, in my opinion, the best of the lot.