The X Files - Deadalive

The FBI is alerted when a young woman is abducted the night before Agent Mulder is discovered near death in a field outside Helena, Montana. Hoping to find a clue to Mulder's possible where-abouts, Agent Scully, Agent Doggett and A.D. Skinner head up an investigation which leads them to a man who says he saves the abductees who are being returned.
Although his claim seems unbelievable, mounting medical evidence causes Scully to fear that newly found abductees who haven't been saved are about to undergo a startling transformation.