Paul and Alva investigate a young Amish girl who shows signs of stigmata, and discover that she is being taken over by another personality. Her family believes the devil has a hold on her, but Alva suspects she may be channeling the spirit of a young suicide victim.
After two young kids spot the ghost of a Confederate soldier, Paul and Keel are sent to investigate. The soon discover that due to certain conditions, the small Virginian town is caught in a time slip, where the past and present are co-exisiting. They soon discover that to settle the soul of the soldier, they must send him a message.
Miracles follows Paul Callan, an investigator of modern miracles for the Catholic Church who questions his faith after repeatedly finding mundane explanations for various supposed phenomena. After he witnesses a true, supernatural miracle that saves his life, only for his findings to be dismissed on a lack of evidence, Paul leaves behind the Church and is approached by Alva Keel to join his organization Sodalitas Quaerito, investigating and cataloguing "unexplainable" phenomena. Along with former police officer Evelyn Santos, Paul and Alva attempt to battle the impending "darkness" before it's too late.