Anime: Rurouni Kenshin (particularly, Son of God arc)
Song: "Believe" by Disturbed
...but lack the episodes anymore (siblings destroyed, and they were lo-qual fansubs anyway :/ ), plus lack the time.
So, if anyone wants to, it could be a very good project. It'd be quite original I'd say; there's not that many Amakusa Shougo tributes out there.

----
Believe, when you lie
You will never need to recognize yourself
To deceive
To remove all chance of doubt and be received
With your lie
The deception is complete when you concede
And decide
To reject your lives, sacrificed to me
Penance can't absolve your sin
Into me
Penance can't absolve your sin
All your belief cannot absolve your sin
Believe, when you lie
You will never need to recognize the source
Of deceit
To renew your faith in God
You must believe, in your lie
The redemption is complete when you conceive
And decline
To release your lives
Sacrificed to me
Reap your life, like you want to recognize, all you've come to
Reap your life
Veiled in shadow
Recognize
Faces of the crucified
I can hear their screams tonight
Ever haunting me
Burn your lie into me
-----
Shougo lies to himself, believing that God is his source of power and thus it is His will to commit atrocities... when in truth such bloodlust can only come from sin. In striving to become like God, he almost wants to usurp Him, and taints His name with good intentions gone awry. Making it look GOOD for Christians to be persecuted, by making Christians appear evil.
Plus what really did it for me was "Faces of the crucified", which could definitely use the flashback of his childhood when he saw Christians crucified by persecutors, and how the bitterness and will for revenge has consumed him ever since.
...It'd sure be nice if someone could pull this off. I'd really like to see it exist someday. ^_^