Enterprise spots a weapon similar to the Xindi weapon that caused the damage on Earth. They detect a ship which is badly damaged and life support is failing on. They take them aboard and they have some injuries. Trip begins working on their ship while Archer talks to the leader of the aliens who say they are on a pilgrimage.
T'Paul, Archer and the alien leader have dinner. He refers to the expanse and the Chosen Realm. T'Paul argues for the side of silence while the alien supports religion. One of the aliens goes to sickbay. Meanwhile the alien leader speaks to some of his followers. They seem to be plotting to take over the ship.
The alien leader goes to see Archer and tells him that there are several of his followers around the ship who are willing to sacrifice their lives using organic explosives and will do it unless Archer turns control of the ship over to him.
After they have taken control of the ship, the alien tells Archer that he is going to use Enterprise to eliminate heretics on his home planet. The alien tells him he has committed crimes by landing on the spheres and he should kill the whole crew. However he says he likes Archer and he thinks he is an honourable man so he tells Archer to select one member of his crew to die.
He also says he must delete all the data and deletes a lot of information from the computers databank. Later Archer is brought reports on the updates. It is brought by the women who went to see Doctor Phlox. She is pregnant and wants to give up the baby as they don't like the way things are going.
The alien tells Archer he looked through his logs and found out about the prisoner interrogation carried out on Enterprise. When the alien asks him, he says he has selected himself to die. However he tricks the aliens and is simply beamed to another part of the ship. He talks to Phlox and then takes one of the aliens out.
The sympathising alien goes down to find Lial with another. Archer takes out the other and makes an appeal to the alien saying this is not his faith. Meanwhile on the bridge a convoy of 4 heretic ships arrive but the alien leader tells the heretic leader they are no match for the Enterprise.
T'Paul tries to stop the alien at tactical from attacking but is held back. Phlox stuns the alien who is guarding him and introduces an agent into the air system which will neutralise the organic explosives. Archer and Reed capture an alien. He tries to set off an explosive but it does nothing. They begin talking out the rest of the aliens.
Archer sends a comm to the bridge saying he has changed command to engineering. Reed leads a team and re-takes the bridge. They hold off the aliens. The alien leader says nothing is important except truth. Arther says he will show him some truth. They head down to the surface of one of the planets - it's a war zone, hardly anything still stands.