I had gone means ero andato

I was gone means I was not there any more  me ne ero andato / non c'ero

Examples:

I had already gone to work, so you did not find me.

Ero già andato al lavoro, perciò non mi hai trovato.

He came but he did not find me, because I was gone.

E' venuto ma non mi ha trovato, perchè me ne ero andato / non c'ero