Police determined that James had been laid by the waist onto the rail, with his upper body on the inside of the tracks. It looked as if his head had been covered with bricks, but the force of the train disturbed the arrangement. The lower half of his body had been carried further down the track.

His clothing, which had been removed from the waist down, was laid near his head. His underwear was heavily soaked with blood. Nearby police found a heavy iron bar, two feet long, with bloodstains, and many bricks and stones with blood. They also found 3 AA batteries near the body. These batteries intrigued the investigators, who had suspicions about their placement before James was hit by the train. A tin of blue paint was also found nearby. James had been severely beaten around the head and neck. There had been fractures, cuts, bruises caused by blows from heavy blunt objects and there had been severe bleeding. On one cheek, a patterned bruise appeared, which indicated the imprint from a shoe. Although there was no conclusive evidence indicating a sexual assault, forensic specialists believed that some of the injuries below the waist were suspicious and sexual in nature.

Even the most experienced investigators were shocked and dismayed by the injuries to James. "You slip into professional mode, but you can never, ever forget," said Kirby, years later. It was bad enough that he had been abducted and murdered, but the beating was brutal, incomprehensible. Although it was common knowledge that a train had severed James's body (the kids who discovered him were already talking to reporters), the police decided to withhold the nature of the James's injuries from the public.