The Doctor manages to deactivate the alarm before the ship blows him to bits. He uses the ship's computer to look up Jex's personal records. Although we don't see the files for ourselves, we do hear the screams and see the Doctor's reaction of utter revulsion. He climbs back out of the ship to find himself face to face with the Gunslinger's machine-gun arm. "I know who you are and I know who Jex is too," the Doctor says. The Gunslinger powers down his weapon. "I don't understand why you haven't just walked into town and killed him," the Doctor says. "People will get in the way," the Gunslinger says. The Doctor agrees that the Gunslinger deserves justice, but suggests they bring Jex to trial instead. The Gunslinger isn't keen on that: "When he starts killing your people, you can use your justice."
Back in town, Jex fears the Doctor has discovered something about his past that even Isaac can't forgive. He plans to escape town by taking Amy hostage, thinking that the Gunslinger won't risk shooting her. Isaac interrupts them.
Back to the Doctor. "No more warning shots," the Gunslinger tells him. "I'll kill the next person to step over that line. Make sure it's Jex."
The Doctor returns to the jail, where Jex is currently trying to explain why he was holding Amy at gunpoint. "It's all lies," the Doctor seethes. "This man is a murderer." He explains that the Gunslinger is a cyborg of Jex's creation, made from volunteers who were never told just what they were volunteering for. Jex tries to explain that their planet had been at war for nine years. The cyborgs he and his team built ended the war in a week. He's quite insistent that he's a war hero. "He's a war criminal," Rory says. "No, he's the guy who saved the town from cholera," Isaac says. Amy thinks they need to find another solution. The Doctor seems too tired to make a decision on his own, so he just goes along with what Amy says. Then Jex has to go and compare himself to the Doctor, which makes the Doctor fly into a rage.