O'Donnell talks of Amy and Martha, establishing she knows more about the Doctor than we first thought. While in the year 1980, she comments that they are pre 'The Minister of War' ... Something to look forward to perhaps? It's in 1980 that they find the ship and the church they are looking for, however the spaceship turns out to be a hearse which will carry the body of the deceased conqueror, The Fisher King. They come across the original ghost from last episode, who is not yet a ghost and in fact, an alien, suggesting that aliens become ghosts as well.
Underwater, the Doctor in ghost form is mumbling a different sequence of words than the previous ghosts. The Doctor is listing all the names of the crew including Clara. Spoiler alert, this is the sequence they die in. Yawn. That was obvious.
The creator of the ghosts turns out to be the Fisher King and it is in fact the Doctor that floods the town, including the church.
Getting back to the opening of this episode, I'm unsure where the writers are going with the introduction of the Doctor as a guitar playing time-lord. Not that I am apposed to a musical doctor. It is the Doctor's speech at the beginning of the episode that he doesn't finish until the very last scene that has intrigued me the most. He toys with the idea that a fictional time traveler composed Beethoven's 5th because of a Bootstrap Paradox - A paradox where an object or information can exist without it ever being created.
So the Doctor asks the question, who created Beethoven's Fifth?
Now that is the Doctor Who we've been missing. The intricate, thought provoking writing we have come to crave. Perhaps this reused storyline wasn't so bad after all.