Context. We can see that the verb following sei requires an auxiliary verb preceding it. Rimasto specifically requires "essere" conjugated depending on the subject. Thus we have "sei rimasto" which translates to "you have remained" or "you stayed."
It means calling on the phone. In this context, that somebody was gone all night, it can mean any kind of communication; meaning the person didn't come home all night and did not text or call on the phone and left the speaker worrying.