Dr. Moraitas is in jail, about to be tried and likely executed for several murders he committed. He tells the policeman who's questioning him that he actually murdered 32 people... and that there are many more left that still have to be killed, in order to make the world safe for the rest of us.
The policeman listens in amusement as Dr. Moraitas explains why he had to kill the 32 people he murdered, and why there's still so much work left to be done. The doctor says there's one simple way to identify people who must be killed, the people who are plotting to destroy the world -- they all have a black scar on each side of their neck. Those are their gills -- they're people from Atlantis, where they've been living under water. The agents of Atlantis infiltrate the surface world with the goal of destroying us. Dr. Moraitas has been trying to kill their agents to stop the evil plot, but now he finds himself in jail, with nothing left to do but try to convince the policeman that his story is true, and that his work must be continued until all of the agents of Atlantis are killed.
"Gem of Purest Ray" looks into the mind of a murderer, and distorts reality. The listener is left uncertain about what's reality and what's fantasy. The story obliterates the line between the two. Delusion and reality merge.
"The ambassadors of Atlantis come from the sea to live beside us, and sew seeds of discontent and hatred among us, wherever we live."
- Dr. Moraitas