"He had come like a thief in the night." is taken from the Bible, specifically Thessalonians 5:2. It refers to the second return of the Lord (Jesus), that means another one from the one we know. The first one is his rebirth after beeg crucified. He will return as "a thief in the night" because we don't know when it will happen, he won't announce it.
the're isn't a word, they're means they are, and there means something is over there. Their means that it is THEIR coat, THEIR pencil. hope i helped :)