So the Alliance troops arrive and storm the cargo bay. The crew of Serenity stand around harmlessly behind the recovered cargo. Simon and River are nowhere to be seen. Mal snarks about the Alliance thinking they're all dangerous criminals or something. Matt arrives and tosses out officious questions. Is this everybody? Mal says that everybody is there, except for the wounded guy they rescued from the cargo ship. Matt sends troops back to the sick bay. Then he asks Mal whether he rescued this cargo as well. Mal has no answer.
Cut down to the sick bay. Two soldiers open the door, but there doesn't appear to be anybody in there. Then they hear a man laughing over in the corner. One turns and looks at him, horrified, but we don't see Peter.
Back in the cargo bay, Matt warns Mal that he could lose his ship for stealing Alliance goods in an illegal salvage operation. He adds that a penalty for such theft would pale in comparison to the penalty he'd face for harboring fugitives. He asks if Simon and River are on board. Mal plays dumb. Matt tries to play good cop, suggesting that nobody would blame Mal if a couple of stowaways had found their way on board without his knowledge. Mal doesn't fall for it. A soldier comes up and whispers something into Matt's ear. Matt tells the crew that they'll continue the interrogation in a more "official capacity." Guards start dragging the crew out of the cargo bay into the Alliance ship as Matt orders every inch of the ship searched. He calls Serenity a junker, which pisses Kaylee off. She calls Matt a "purple belly." Whuh? Their uniforms are gray. Let me guess -- the Alliance wore purple during the war or something. While the crew is being forced off, Alliance doctors unload Peter on a stretcher. We don't get a close enough look to see what has happened to him yet.