Shawn and Gus know they are missing something, so Shawn climbs the tree and they run through the murder again. When Nelson fell from the horse, he rolled way passed his mark. He wasn't supposed to land anywhere near the tree. Seeing the killer up there was an accident. Nelson wasn't the intended victim. He only interrupted a plot to kill someone else. From his position in the tree, Shawn has a perfect sightline to the medical tent, and where Sally Reynolds was standing. The intended target was Sally, which means someone is still trying to kill her.
The murderer could be anyone in the regiment, so Shawn and Gus steal Sally's uniform and decide to stand in for her and wait for the killer to strike again, catching him in the act. Juliet stands in for Sally but as the battle wages on, nothing happens. No one makes a move.
Shawn and Gus check the other side of the camp, where they discover Mahoney's uniform in the Confederate tent – and it's missing a button. Mahoney is the killer! Just then, they hear a blast of C4, and it didn't come from the battlefield. It came from the direction of Mahoney's store. He's there right now and not on the battlefield as everyone believes. It turns out, Mahoney and Sally were in on a plot to rob the store, using the battle as cover, and split the insurance pay out. But Mahoney got greedy and decided to kill Sally and keep the money for himself. With Mahoney and Sally arrested, Shawn and Gus happily return to comforts of the year 2006.