The episode narrative speaks to the true-church narrative:
D’JAMAT: For the last century, a violent group of heretics have tried to undermine our way of life. With your ship I can deliver a final, decisive attack. I can end this conflict forever.
ARCHER: A war. That was the glorious mission you were talking about?
D’JAMAT: I’m trying to save my people.
ARCHER: Why do I have the feeling these heretics would say the same thing.
D’JAMAT: They might very well, but it doesn’t change what they are. Enemies of the truth.
ARCHER: Your truth.
D’JAMAT: There’s only one.
ARCHER: How many people do you intend to kill with my ship?
D’JAMAT: Your species is obsessed with numbers. A characteristic of your misguided belief that the secrets of the universe can be revealed through science. This may sound barbaric to you, but it doesn’t matter how many heretics die. When the Makers return, only the faithful will survive. Non-believers will be swept away. Not only Triannons, but every race within the Chosen Realm.
…
D’JAMAT: I sympathise with you, Captain. I’ve had to make hard choices as well. When I was young, I fought with the Holy Regiments. I was commanding a mission. We’d infiltrated a village known to be a heretic stronghold. We were instructed to stay concealed and relay intelligence about enemy movements, but one of the villagers discovered us. It was a small boy, no more than six years old. We knew if we let him go he would alert the village, and if we tried to hold him he might give us away. There was only one action to take, so I took it.
ARCHER: You’re proud of that.
D’JAMAT: In the service of the Makers, all actions are blessed ones.
ARCHER: There are no Makers. At least, not how you perceive them. The Spheres are machines built for a reason you and I don’t understand.
D’JAMAT: I was once like you, but then I felt the Breath. I prayed for you, Captain. I had hoped that the Makers would open your eyes to the truth, but it seems that they’ve turned away.
…
D’JAMAT: I know you too well. Tell me what’s wrong.
YARRICK: We’ve just begun this mission and already three people are dead.
D’JAMAT: And that bothers you.
YARRICK: Shouldn’t it? These people are not our enemy.
D’JAMAT: They are non-believers. That makes them our enemy.
YARRICK: Why?
D’JAMAT: Do you believe the Makers speak through me?
YARRICK: Yes.
D’JAMAT: Then when you question me, you question the Makers, and there’s a word for that. Heresy.
Yarrick, when you begin to sympathise with the enemy you risk becoming the enemy.
…
YARRICK: You can’t win. They’ll destroy the ship.
ARCHER: Not if you help me.
YARRICK: No.
ARCHER: You know this is wrong. Everything he’d doing, we can put a stop to it. All of it.
YARRICK: I won’t betray my faith.
ARCHER: Your faith betrayed you. Is this really what the Makers want? To kill people by the thousands in their name? Is that the faith you were raised in?
YARRICK: No.
ARCHER: Then do what’s right. If you don’t help me, you’ll be condemning your wife and child to death, because that’s how this is going to end. As long as people like D’Jamat dictate what’s true and what isn’t, all you’ll ever have is war.
…
ARCHER: These people you’re fighting. What makes them heretics?
YARRICK: We believe the Makers created the Chosen Realm in nine days. They believe it took ten.
ARCHER: For that, you’ve been at war for over a century?
