HAD GONE ALREADY indicates that there are to events in a sequence and that they occurred in a time now past; the already adverb speaks of the event have been completed.

Joel rushed to his boss's office, but she had gone home already. THIS IS JUST FINE. THE EVENTS ARE GIVEN A SEQUENCE AND ORDER OF OCCURRENCE. HIS BOSS HAD LEFT BEFORE JOEL <RUSHED> INTO THE OFFICE

Can i say: Joel rushed to his boss's office, but she went home already. THIS IS ALL WRONG BECAUSE THERE IS NOT INDICATION OF A CONNECTION BETWEEN THE TWO EVENTS

HOPE THIS HELPS