It culminated with the Doctor finding out that recurring character Missy was a female incarnation of his arch-enemy the Master.
But some viewers found the plotline, about death and cremation, disturbing and complained to the BBC.
The BBC's officially responded and has defended the episode.
The BBC said: "Doctor Who is a family drama with a long tradition of tackling some of the more fundamental questions about life and death.
"We were mindful of the themes explored in Dark Water' and are confident that they are appropriate in the context of the heightened sci-fi world of the show."
The episode featured an organisation called 3W (standing for Three Words) which offered the slogan "Afterlife means after care".
As part of the plot, some of the characters discussed what may happen to people after they die.
The BBC said:  "The scene in which a character reveals 3W's unconventional theory about the afterlife was preceded by the same character warning the Doctor and Clara several times that what they were about to hear could be distressing.
"When the Doctor does hear these claims, he immediately pours scorn on them, dismissing them out of hand as a 'con' and a 'racket'.
"It transpires that he is correct, and the entire concept is revealed to be a scam perpetrated by Missy."
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Doctor Who's most recent episode was the first in the two part finale of the latest series.