Hiraga Joseph Kou and Roberto Nicholas are sent in San Rosario's abbey in Northern Mexico to investigate about a supposed immaculate conception of a young nun, sister Dolores. That same night, however, one of the abbey's priests is found horribly dead, and shortly after a new apparent miracle occurs.

The miracle of the stone's tears is easily explained, but new murders taunt San Rosario. Joseph and Roberto think that part of the answers could lie in the abbey's ancient history, but the other priests' hostility doesn't allow them to investigate further.

Dark secrets emerge from the past while Joseph and Roberto keep on investigating about the chain of deaths in San Rosario. Meanwhile, a supposed demonic possession proves to be something much more terrible, under which the two Vatican priests start understanding the true nature of San Rosario.

Joseph and Nicholas have finally discovered the truth about the supposed Immacolate Conception, which lies in the final days of the World War II, when from the asces of a dying Third Reich someone was already spreading the seeds for the birth of a Fourth one.

While remembering his first meeting with Lauren, Joseph reminds of an old case still under investigation after many years: the case of a man and a bet with the Devil. Can an infernal gift be used for good purpose and the seek of happiness?

Joseph and Roberto travel toward Central Africa to investigate a case of incorruptible body of a longtime dead clairvoyant, father John Jones. First analysis seem proving the miracle, as much as the true gift of the deceased priest. However, while Joseph is fascinated from the holy spirit of the church's main priest Julia, Roberto at the opposite sees in Jones' last prophecy a dark fate waiting for him.

Roberto's desperate resarch to explain the miracle, and so avoid the propecy about his imminent death, will reach the point that his own soul, more than his life, will be put at risk.

Despite Roberto's salvation, the miracles around John Jones' prophecies and incorruptible body seem above any doubt. However, the truth lies right in Roberto's childhood, and what seemed to be the most holy spirit will prove being something completely different.

Countless miracles seems to happen in a small village near Florence, Italy. Joseph and Roberto, while investigating them, find traces of an old and obscure legend: the Headhunter Clown that haunts the woods around the village.

Joseph and Roberto's personal investigations about the murder in the church soon find a connection with a old case happened in 1985. Meanwhile, Suskins reveals that a probably still alive Julia the Headhunter Clown and Galdoune may be connected.

Following the same route of the unfortunate 1985's expedition, Joseph, Roberto, Suskins and Bafi ultimately find Galdoune's hideout. However, after having discovered the organization's true ambitions, the two priests' faith is dramatically put on test: are they ready to sell their souls in exchange for seeing their deepest dreams realized?

While facing his appearently last moments on Earth, Ryota starts thinking about his life, signed since childhood from three hooded men visiting him each time someone close to him was at the point of death. There will be place for a true miracle this time?

The flyer from this year's AnimeJapan 2017 event revealed that Vatican Kiseki Chousakan will receive an OVA episode.