What do they find inside the church?

A Dalek ship

Fortunately for Martha, the church was empty but she still had visions of running into somebody -- a minister, a choir member, an organist, etc. -- who would not appreciate her nakedness. Or worse yet, she feared running into someone who would appreciate it too much.

Then the doctor veered off toward a door that seemed to lead toward the church basement.

Good, thought Martha. At least we're less likely to run into someone down here.

"Oh my," said the Doctor. "Somebody hid a ship down here."

"A ship?" asked Martha.

She glanced at the round silvery object the Doctor was pointing to and saw that it did kinda look like a small space ship. Or better yet, a flying saucer. Whatever it was seemed large enough to have carried at least one regular-sized human being. Maybe two, if they were lucky. And yet Martha got the feeling that it was not humans that had used this ship.

"Judging from the size and shape," said the Doctor, "I'd say this ship originally came from the planet Skaro. Which means this is most likely a Dalek ship!"

"What's a Dalek?" asked Martha, forgetting her nakedness for a brief while.

"A member of a self-proclaimed master race of xenophobes who are among the most vicious creatures I have encountered," said the Doctor. "They have enslaved whole worlds and those people that they can't enslave, they kill. By the thousands."

Martha felt a chill go up her spine that was not caused by her lack of attire.

At that moment, she heard a voice behind her say, "Thank God you showed up."