Learn Italian: Sembrava che avesse scoperto il complotto. - It seemed that he had discovered the plot.

The main verb sembrava (it seemed) is in the past tense and expresses an appearance or uncertainty, which triggers the subjunctive mood. Because the discovery happened before it seemed that way, we use the pluperfect subjunctive (trapassato congiuntivo) to show that this action happened further in the past.

Since the subject pronoun isn't there, how do we know it means 'he had discovered'?

The helping verb avesse is the third-person singular form of the imperfect subjunctive, so it can mean he, she, or formal you (lui, lei, or Lei). The I and you forms are both avessi, so it cannot refer to them. In a real conversation, previous context would tell you exactly who it refers to.

If the subject were feminine, would scoperto change to scoperta?

No. The verb scoprire takes avere as its helping verb. Just like in standard past tenses, verbs conjugated with avere do not change their past participle endings to match the subject. It stays scoperto regardless of who is doing the discovering.

Is scoperto an irregular past participle?