I could've sworn I'd ranted here about some writers' inability to use the past perfect tense properly, but a quick search suggests I haven't. So here goes the latest in a long line of grammar mini-rants.
Everyone understands the simple past tense. "I did X." "She went to the store." "Eddie flew over Khartoum."
But the most common narrative convention in modern fiction is to tell a story in the past tense. And when you want to refer to something that happened before the past-tense "now" that the story is taking place in, you have to indicate grammatically that the two past times are different.
Luckily for writers, there's a standard way to do this. Past perfect is a tense usually formed (in English) using the word had with a correctly conjugated main verb: "I had done X"; "She had gone to the store"; "Eddie had flown over Khartoum." Past perfect is used to indicate "an action or state [that has been] completed at or before a [particular] past time," according to MW10. In other words, if you're telling a story in past tense, and you want to talk about an action or state that's completed, over and done with, by the time of the main story, you use past perfect.
This should not be a difficult rule to follow. Most people in ordinary speech use past perfect naturally, even if they don't know that's what they're doing. (I didn't know what the term past perfect meant until a couple years ago, but I knew how to use it.) "I bought eggs on the way home, but it turned out Jean had already picked up eggs the night before." But when it comes to fiction, an awful lot of writers don't seem to recognize how past perfect should work. I see a remarkable (to me) number of stories in which simple past is used throughout, even when referring to events that took place before the story begins.
So here's an easy way to think of it: in most stories written in past tense, there are two possible times that a given phrase could be referring to. One is the "now" of the story; use simple past for that. The other is any time before the "now" of the story; use past perfect for that. To use past perfect, attach "had" to the verb, and then figure out what form of the verb sounds right with "had."
You will make your editors a much happier lot, which will make them more inclined to accept stories, perhaps including your own. (Then again, if they get too happy, they may decide to sit in a field all day plucking daisies, which will result in no stories being purchased. So be sure to format your stories a little bit badly to keep your editors a little bit grumpy. It's good for 'em.)
The other important use for the past perfect is to ease transitions into and out of flashbacks, but that's a more advanced lesson, and one I'll save for another time.
Don't even get me started on present perfect and future perfect. (But those are much less commonly needed than past perfect, so they're much less commonly a problem.)