The "had done" form (or past perfect) is one of the least used tenses in English. We only really use it in the following situations.

* When it's important to say which event happened first in the past

* In reported speech

* To show regret about the past

* In conditional (if) sentences

Normally, when we say what happened in the past in English, we use the simple past or past continuous form.

For example, "He got up early to go to the beach. He spent all day there and went home as it was getting dark."

We know which order things happened in, so we don't need the past perfect tense.

Sometimes, we need to explain which events happened before other ones (especially if we "jump" around in our story). When we need to show that one thing happened before another, we can use the past perfect form.

For example, "I was hungry, as I hadn't eaten all day." (Being hungry happened after not eating all day.)

Compare these two sentences:

"When he got to the airport, the plane took off." (The plane took off after he arrived at the airport.)

"When he got to the airport, the plane had taken off." (The plane took off before he arrived at the airport.)

Reported speech in English

"I didn't see her," he said.
Because his words are in the past, when we report them we need to go one tense back and use the past perfect.

"He told me he hadn't seen her."

This is also the case if the words are in the present perfect.
"I have never been to Scotland."
She said that she had never been to Scotland.

To show regret

I wish I hadn't gone to the party. (But I went.)
If only she hadn't bought that car. (But she did.)

Conditional sentences (when we speculate about past events)

If I had worked harder, I would have passed the exam. (But I didn't work harder, so I failed.)

If you had told me, I could have helped. (But you didn't tell me, so I couldn't help.)

If they had left earlier, they might have caught the plane. (But they didn't leave earlier, so they didn't get the plane.)