A Chaplain is an officer with religous/clergy credentials. There are chaplians from all the major religions.
They perform religious services; but in addition to that they have a responsibility to watch after the spiritual and emotional well being of the members. From my experience many of them will tailor their counseling to jive with the spiritual views of the person; I have also heard stories to the contrary.
One thing about chaplains - whatever you say to them is completely confidential, as opposed to your chain of command, ADC, mental health, family center.
In a world moving more and more towards secularism many people call into question the relevancy of the US military chaplain.
You go to Area Defense Council or ADC. The JAG or staff judge advocate is there to prosecute you. Also I have sought counseling from Chaplains and I am not the devout sort. I have never met a chaplain I didn't like.