In your example: "After he had eaten breakfast, he went to work."

"had eaten breakfast" happened first.

"went to work" happened second.

Had + Subject + Past Participle of the verb +...?

* "had" and the past participle.

In the example provided: "After he had eaten breakfast, he went to work," the action of "having eaten breakfast" happened first

Had+subject+past participle of the verb+....?

In other words, "already" emphasizes that something had already happened earlier than expected or before another past action.