When and why a writer should use the past perfect tense?

Past perfect is used to show one thing in the past happened before another thing in the past. This other thing in the past is usually expressed by past simple. eg

The train had left when I arrived at the station.

Had left is past perfect and this event happened before arrived which is past simple.

So you would use past perfect when telling a story about things in the past. eg

I felt really tired when I took the train to work yesterday because Sophie and I had been to a party the night before. We hadn't gone to bed until 3:00am. I had been on the train 5 minutes when I realised that I had left my wallet at home. I phoned Sophie but she had already left for work.