We use past perfect to provide a history or explanation to the main events in a story (the main events being expressed in past simple). When the past perfect comes after the past simple event that it refers to, you can imagine the past perfect as a kind of "movie flashback".

In simple terms, you use it when you are referring to _two_ times in the past. The time when something happened, and a 'reference time'. You use the tense to establish the relationship between those two times. The reference time can be explicit, or it can be implicit.