The pluperfect subjunctive

Since the "past subjunctive" is not a true past tense, it uses as its past tense what is structurally its perfect aspect form. This past tense is known as the past perfect subjunctive or pluperfect subjunctive; it is formed using had (the past subjunctive of to have) plus the verb's past participle.

The pluperfect subjunctive is used like the past subjunctive, except that it expresses a past-tense sense. So, for example:
If I had known (yesterday), I would have done something about it.
If I had seen you, I definitely would have said hello.
I wouldn't be here if he hadn't helped me.

If a clause is in a past tense, then a clause subordinate to it cannot be in the past subjunctive, though it might be in the pluperfect subjunctive; however, if it is in a present tense, then a clause subordinate to it might be in either of the two, depending on meaning.

All that said, the pluperfect subjunctive is often replaced with the past subjunctive in colloquial speech, a substitution that is commonly considered incorrect. (See prescription and description.)

(Note that by contrast, the present perfect subjunctive — that he have done — while logically and theoretically possible, is not much used in modern English.)