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.
He drags Jex from the jail, chases him through town and then shoves him over the borderline. Where just moments ago we saw him championing the legal system, the Doctor is now all about making the judgment himself. When Jex tries to cross back into town, the Doctor grabs a gun. He aims it at Jex's face. Isaac calls his name and the Doctor spins around to face him, gun still at the ready. Suddenly Amy has a gun of her own. She shoots into the air. "Let him come back, Doctor!" It's a demand, not a plea. This moment of seriousness is interrupted when she keeps accidentally firing the gun like she's Homer Simpson. Then it's serious again as the Doctor goes off on a rant. "Every time I negotiate, I try to understand, well, not today. No. Today I honor the victims first -- his [points at Jex], the Master's, the Daleks -- all the people who died because of my mercy!" Amy stays calm. "See, this is what happens when you travel alone for too long." He should really look into getting another dog. Amy tells him they need to be better and it finally reaches the Doctor.