Episodes 9 and 10 of season one form a two-part episode: The Empty Child and the Doctor Dances
This still remains one of my favorite episodes of Doctor Who. I did not know this at the time, but it was written by Steven Moffat. Moffat has written many of my favorite episodes, including "The Girl in the Fireplace," "Blink," and much of seasons 5-7. Moffat is more into the fairy tale aspects of story telling.
In this episode, the Doctor and Rose are in London during the Blitz in WWII. We get the introduction of Captain Jack Harkness, who will become a regular on the series and the star of the spinoff Torchwood. Harkness, a former time agent (what?) turned con man, saves Rose from falling to her death during the Blitz. He then proceeds to try and seduce her, but his angle is primarily a con.
The episode is high on the creep factor. The creepy comes in the form of a little kid with a gas mask who keeps repeating, "are you my mommie?" This child can make telephones ring, radios blare, even if the telephone is not connected (like the phone on the Tardis police call box). Moreover, people all over the area are developing "injuries" that match those of the boy. Namely, they are replicating his physical injuries, as well as growing gas masks out of their very skin. The implication, given time, humanity will be reduced to a bunch of walking, mommie-spouting, zombies with gas masks.
There is not a lot of fodder for religious/sci-fi intersections. The Doctor figures out the problem: the alien tech nano-genes that crashed on earth are doing their best to "heal" the human race, but the best model of the human race that they have to work with is this little boy who was killed during a bombing raid while wearing a gas mask. With this genetic information, they nano-genes are repairing all with whom they come into contact by replicating the state of the boy.
The Doctor figures out what is happening, but does little beyond making the solution possible. He introduces the nano genes to the boy's mother, and hopes that they will recognize what a human truly should be like. They do, and the true healing commences. At the end, the Doctor revels saying "everybody lives." Life triumphing over death is the greatest possible outcome for the Doctor.