gone with be

Gone can be used like an adjective after be, to say that somebody is away, or that something has disappeared or that there is no more.

• She’s been gone for three hours – what do you think she’s doing?
• You can go out shopping, but don’t be gone too long.
• When I came back my car was gone.
• Is the butter all gone?

note

For been used as a past participle of go or come, (see here).