In the episode “The Underwater Menace,” the Doctor, Ben, Polly, and Jamie arrive in the lost underwater city of Atlantis. The situation they find their combines the worst of both religion and science. Soon after arriving, the travelers are nearly sacrificed to the “living goddess Ando” who is depicted as part human, part fish. They are rescued when the Doctor sends a note (which he signs “Dr. W”!!!) to a professor he has figured out is there, Professor Zaroff, saying that an important secret will die with him. Zaroff turns out to be quite mad, having promised to raise Atlantis from beneath the sea, when in fact his plan is to lower the sea in a way that will split the planet, destroying the world. We thus have what is depicted as superstitious and primitive religiosity on the one hand, and the stereotypical mad scientist on the other.
The Doctor remains throughout a man of science. As one could have predicted, the Doctor and his friends manage to stop Zaroff. Because he had worked both to stop Zaroff and also save the Atlanteans, when they think the Doctor may have died in the process, the Atlanteans consider how to honor him appropriately, one suggests a monument in a rebuilt temple. But their leader rejects this idea, saying that it was gods and superstitions that allowed them to be manipulated as they were, and so he suggests that rebuilding Atlantis without temples or gods would be a more fitting tribute.
Of course, one should not oversimplify the matter. In the very act of traveling through time and space in a seemingly magical police box, and visiting a city that is myth rather than reality, the lines between magic and science, and between religious and scientific forms of delusion and madness, are once again transgressed.
This is one of the lost episodes of which a part was recently rediscovered, and so here is a clip: