The story follows Fathers Josef Kou Hiraga and Roberto Nicholas who, under the Vatican's orders, work to unravel mysteries involving so-called 'miracles'. Despite being ordained priests, they use scientific methods and logical reasoning to disclose the truth about the alleged holy events that they investigate.
Vatican Miracle Examiner has examples of:
- AB Negative: Very conveniently, this is Sister Dolores' blood type.
- Abusive Parents: John Bricket's parents. Also, Roberto's father.
- Ancient Conspiracy: Galdoune, which apparently has ties to The royal line of Bourbon
(in Real Life, thought extinct by 1521) and The Illuminati, and is cutting-edge in the production of drugs, forged dollar bills, cloning and medical science, specifically wanting to control the world through the last mentioned in the long run. Preparations for this conspiracy's grand plan include subjecting a small population of Italians to 800 years of deprivation from sun-light and gold mining to see how they would end up. It's clear that Galdoune is very fucked up, and very dangerous, potentially poised to Take Over the World. - Anime Catholicism: Downplayed, but still felt due to the excessive femininity of some male characters, and the and overly stylish Christian symbolism in the series.
- Apocalypse Hitler: The anime's first 4 episodes in a nutshell.
- Artificial Human: Father Julia was the sixth of such produced by Galdoune attempting to genetically engineer the perfect human being.
- Artistic License – Geography: St. Rosario's Church is said to be located in some unspecified country of South America. However, the map that shows the route taken by the plane points to somewhere in Mexico.
- Artistic License – Biology: There is no such a thing as a virus that turns your blood into a rubber-like material. But, even if it were, its effect would be a increased risk of thrombosis due to blood hyperviscosity, and not a non-decaying body. Also, being sun-deprived can never make one turn albino. Albinism is a genetic, inherited condition, not an acquired disease. You are either born with it or you will never have it.
- Badass Israeli: The organization of the Zion Code in episode 4 is almost a direct reference to Jewish secret organizations of Nazi hunters, whose goal was to track down Nazi criminals after the war.
- Bad Santa: On the Christmas day (which also happened to be the day of his thirteenth birthday), John Brickett lost his neighbour friends, killed by a man dressed as Santa Claus.
- Be Careful What You Wish For: John Bricket learns this the hard way. First he wishes he wouldn't have to see his abusive mother ever again and his mother dies seconds later. After he wishes his mother would be alive again, she miraculously comes back to life but as a completely different person.
- Big Red Devil: A recurrent trope on the first arc, along with its inseparable partner, the Number of the Beast.
- Blind Mistake: The guard of St. Rosario's Academy suffers from a very rare condition called Riddoch Syndrome. Father Hiraga easily diagnoses it, despite having no medical training.
- Body Double: Father Julia has (or better said, had, since the poor thing died in his place) one. The true identity of his double wasn't revealed, and it was only hinted that he probably lived locked in a room full of toys. Later, Julia confessed he was his "twin brother", or rather a clone.
- Body of the Week: Bodies, in this case - there is more than one gruesome death per episode.
- Bookcase Passage: Below the glass case where the Holy Lance is displayed in St. Rosario's Church, there is a staircase that leads to some sort of chemistry industry intended for producing illegal drugs. On another episode, behind Father Julia's painting, there was a secret chamber leading to a child's room, a corridor with shelves full of jars containing human hearts inside, and an operating room with a pentagram drawed on the operating table, where an Ancient Conspiracy with ties to The Illuminati (yes that one) had a woman give birth to a Siamese twin they call "Janus" - yes, this series never stops trying to overcome itself on macabre things.
- Boom, Headshot!: How James Chester ended up dying.
- Church of Saint Genericus: Completely avoided, as the place where the action develops in the first four episodes not only has a name based on one of Virgin Mary's titles (St. Rosario's Church), but also has the interior decorated with stained glass windows depicting Saints and Martyrs who are properly named.
- Clueless Mystery: The anime's breakneck pace and the amount of information dumped onto to the viewers allows no time for anyone try to figure out what is happening.
- Conjoined Twins: A more feasible explanation to Mary Brown's deceased child(ren). Makes a lot more sense than the baby(ies) being an incarnation of ancient deity Janus (who is depicted as having two heads), right?
- Deal with the Devil: Julia's offer to Hiiraga and Roberto is framed like this after they're captured while snooping around in Galdoune's underground tunnelwork; Galdoune has genuine Villain Respect for the investigators, and no findings of theirs in the old tunnels they were in could ever threaten the Ancient Conspiracy. So instead of killing two gifted young men in their prime, Julia offers them both what they always wanted in return for them joining Galdoune.
- Hiiraga has spent most of his teenage and adult years frantically searching for a cure to his brother Joseph's terminal disease. Galdoune are pioneers in the medical field and already have an off-market wonder drug they are 100% certain will work on poor Joseph.
- Roberto has always been obsessed with old tomes and lost knowledge. Julia makes it abundantly clear that Galdoune are incredibly impressed with Roberto's abilities as a translator and offer him all the time, resources and staff he would ever need to go through the group's 800+ years worth of archives with many, many books of theirs in need of copying down or being re-translated.
- Due to their mutual disgust for Galdoune's methods, both naturally refuse. As a token of good faith, Julia still went on to disguise himself as a civil doctor and personally delivers and administered the drug to Joseph, who did recover as promised.
- Dude Looks Like a Lady: Several characters, but Father Julia in particular. His bisexual superior within Galdone says he enjoys partying with Julia most of all people because he gets to see the bishie in pretty dresses.
- Evil Parents Want Good Kids: Azazel gave to his only son 1000 wishes which would be immediately granted, as a way of testing humanity. Depending on John's choices, humanity either would be wiped out or spared.
- Faking the Dead: Father Julia, on episode 8. What motivated him to do so remains a mystery.
- Fantastic Catholicism: Easily guessed by the title, the series has lots of references to Christian iconography and imagery.
- Fetus Terrible: Both of Mary Brown's children. Averted with Sister Dolores' child.
- Fictional Country: Sofuma, a typical example of Darkest Africa.
- Four Eyes, Zero Soul: Lauren Di Luca
- Gratuitous Nazis: The resolution to the first mystery could have been, with a little more of creative effort, almost credible, if it weren't for the fact that the Church's illicit activities producing and distributing drugs were performed by Priests who were actually second- and third-generation Nazis.
- Ghostapo: The Reveal of the first arc of the anime is that the priests at St. Rosario Church turn out to be Nazi occultists who believe in Hitler as the Messiah and worship Satan under the influence of drugs.
- House Husband: Roberto and Hiraga aren't technically a married couple, but one of their very first interactions on episode 1 was Roberto ironing Hiraga's cassock. Then, on episode 5, Hiraga boasts to a less-than-amused Lauren Di Luca how amazing at performing chores Roberto is.
- Jump Scare: The most delightful scene of episode 3 involved the sudden appearance of a masked person holding a knife to Father Nicholas.
- Kill It with Water: Subverted, as Father Hiraga candidly explains that his bottle of "Holy Water" contained a very different fluid. Meaning sulfuric acid. Just in case.
- Medical Rape and Impregnate: Happened first to Mary Brown, and then, a few decades later, to Sister Dolores.
- Not Quite Dead: Father Thomas, who survived being burned alive only to perish by Multiple Gunshot Death.
- Nun Too Holy: One of the most discussed moments of the first episode was that in which Sister Dorothea bites into a sausage in such a explicitly sexual way that even the more chaste viewer could not notice. Turns out she was NOT actually a nun, but a spy from Zion's Order who infiltrated St. Rosario with the intent to uncover the Priests' plan of creating a new Nazi Reich.
- Ominous Latin Chanting: The BGM is heavily influenced by Gregorian chants, and Ave Maria tends to play even during sequences in which nothing sinister is about to happen.
- Ouija Board: The students from St. Rosario's Academy seems to enjoy indulging in seances that include, of course, trying to talk with the Evil by means of using a curiously crafted Ouija Board that has an alphabet derived from the Runes.
- Pedophile Priest: The reason for Carlos' odd behaviour upon hearing about Father Klaus' death was that the student was being sexually abused by Father Klaus and a few other priests. When Hiraga and Nicholas came to St.Rosario, Klaus feared he would be exposed and threatened Carlos with death had he dare to tell anyone.
- Real Men Cook: In addition to being a scholar on the matters of theology, history, syncretism and being a near Omniglot, like any proud Italian man Roberto is a wizard in the kitchen, and he and Hiiraga will discuss the episode's happenings over dinner after the ED.
- Religion of Evil: The students of St. Rosario Academy are constantly being caught performing some obscure rite in the middle of night, and rumours are that there are devil worshippers among them. This trope magnified to a even larger level as it was revealed that the whole Academy was run by former Nazis whose sole purpose was brainwash the students into creating a second Nazi empire.
- Religion is Magic: Surprisingly enough, averted, since the investigated 'miracles' are explained by science - a misrepresented and far-fetched science, though. One of the early examples, a weeping state of the Virgin Mary, turns out to be caused by condensation - the stone statue was chilled from being washed in an ice-cold fountain.
- Scaled Up: while under the effect of the poison of a black mamba, Roberto sees himself being trialed by Atotelus, a made-up Snake God.
- "Scooby-Doo" Hoax: The main premise of the series is that many "miracles" are either a confluence of random scientific circumstances, or a deliberate hoax of swindlers.
- Snakes Are Sinister: for sure they are. It doesn't matter if it's just a painting or if it's the real thing, the evil aura that emanates from them will give you a chill down the spine. Thank God (or should I say thanks to Hiraga) Roberto doesn't end up dying victim of one - his partner was shrewd enough to order some antivenom through the mail just in case Roberto gets bitten.
- Suck Out the Poison: Hiraga does this to Roberto supposedly to prevent the black mamba poison spreading through his circulation. Anyone with a little knowledge on first aid for snake victims knows this is not only ineffective, but also potentially dangerous. Also, why lose your time sucking the venom when you already have the venom antiserum at hand? Makes no sense.
- Through His Stomach: The ending of every episode shows Roberto cooking something up and then eating together with Hiraga in their Vatican clergy dormhouse. Also, on episode 5, Hiraga comments enthusiastically about Roberto's abilities on the kitchen to a seemingly jealous Lauren Di Luca.
- Villainous Rescue: the last turning point of the rollercoaster plot that were VME was Julia saving Hiraga’s brother, Ryota from iminent death. Talk about a miracle...
- White Hair, Black Heart: Father Julia.
- Whole Episode Flashback: never before in a series the Flashback Within a Flashback trope was so abused as in VME episode 5. Also applies to episode 12.
