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.
Here, then, we see the Doctor as more like the enlightened crew of the starship Enterprise than ever before. He does not merely see through superstition, but undermines it, working even if indirectly towards the elimination of gods and temples. This is a facet we will see revisited in a similar way in other episodes in the show’s history, such as “Planet of Fire” in the Peter Davison era. And in later times we will find that the Doctor did such things in a manner at odds with the time lords’ equivalent of the “Prime Directive.”
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: