"gone", mostly in the form of "He (or she) is gone" or (less often) "he has gone", is a common euphemism for "He is dead" or "he has died". Both may be and often will be contracted to "he's gone" (or she).
This is normally phrased in the passive voice, which omits the cause and agent of death. Often the cause is not known, and even when it is, when the speaker is using an euphemism, the speaker often prefers not to specify the exact cause.
In police procedural novels, and medical thrillers, it is very common for someone to check the pulse and heart action of an injured or ill person and say "he's gone" or "he is gone" in the present tense, meaning that the person has just died. I believe this reflects the actual usage of real medical and police personnel.
This figurative meaning of "gone" should not be confused with more literal meanings, where it indicates actual movement, although it may ultimately be derived from "He has gone to Heaven" or a similar image. "Gone" is less likely to be used for died when the death is not quite recent. Other euphemisms, such as "passed", are in my experience more often used in that situation.
Some people, of course, prefer to avoid any euphemisms, and will say "he died", "he has died", and "he is dead" (depending on the tense of the overall statement). (Of course, "she" can also be used in any of these cases.)
There can be cases where this use of "gone" is ambiguous, but in practical terms, it is almost always quite clear when the speaker means "he is dead".