Doing In the Wizard

"It's like finding out that pixie dust is just a fungus which grows in the brain."

- The Distressed Watcher

Removing a relatively poetic or mystical element (or possibility) and replacing it by way of Retcon with a more "realistic" one, in a Revision, sequel or other adaptation, or occasionally even just later in the same story. This is pretty common in a fantasy-to-Sci Fi situation, probably because the two aren't too different in the outcome produced -- a magical invisibility ring vs. a technological cloaking device are functionally the same. However, it tends to disgruntle fans of the original, especially when the explanation is less satisfying than the mystery. Amusingly, if the answer is in Techno Babble, its "reality quotient" is just as silly as the initial explanation. It can also demand a whole sequence of coincidental oddities, which (as observed by Aristotle) just makes it less convincing.

Another problem this trope might encounter is that, while fans only expect magic to have the same effect while used in the same way, the audience may be less willing to suspend disbelief when converted into hard science, unless it is prefaced with some kind of pseudoscientific material specifically stated not to follow standard physics (of course, doing this still keeps the stuff technically magic, just not, you know, magic).

Compare and contrast with How Unscientific. See also Demythtification, The Magic Goes Away, and Magic Versus Science. Diametric opposite to Doing in The Scientist. Inbetween you have Maybe Magic Maybe Mundane. Compare Jossed. Contrast Magic a Is Magic A.

Anime and Manga

 * Jo Jos Bizarre Adventure has two completely ridiculous examples. The first is a mystical stone mask that turns its wearer into a vampire when exposed to blood, by grabbing their face with spikes; it's said to work by hitting key pressure points. The second series reveals that the mask was actually created by an advanced race of humanity that eats vampires. The second is when it is revealed that Stands (Psychic Powers personified) are created through a magical arrow forged from a meteor, which grants a Stand to anyone it hits. This arrow is later revealed to be not magical, but radioactive, and grants Stands by mutating the target's DNA. Given that the entire franchise runs on the Rule of Cool, most fans just smile, nod, and wait for the next fight scene.
 * The functionality of the Stone Mask was never explained though. The thing about pressure points was just Jonathan's theory and he was unaware of the mask's supernatural qualities at the moment.
 * Also the nature of the Arrows is left rather ambiguous as well (the less-than-accurate translation certainly didn't help the subject), while claims it's an extraterrestrial virus that creates the effect of the arrows' material, it's made very obvious that they seem to have a will of their own and a more spiritual quality to them. The supernatural side is also present in Part 6, making the whole Doing In The Wizard controversial at best.
 * Mazinger Z and Great Mazinger: In the Mazinger versus Great General of Darkness, a prophet warns Boss and his gang -and later Kouji and his friends- about the inminent Mykene invasion. It turns out that
 * And in the episode 36 of Mazinger Z, a witch.
 * Dragonball revealed that two mystical-seeming main characters were actually aliens about half way through the series. And everything above other than the man-wolf has been hand waved as "ki". Wizards have been exposed as using ki power and advanced technology.
 * Toriyama only bothered to sci-fi up those elements from early Dragonball that he actually remembered to keep using after the time skip that led to "Z." Stuff like Launch's transformations, the Flying Nimbus/Kinto'un, and Baba's witchcraft were never anything other than magic. Even the title Dragon Balls themselves are not technological: they may be ALIEN magic now, but they're still magic.
 * One Piece is known for doing in certain cases once the Straw Hats reach the Grand Line. The mysteries of Skypiea and the Florian Triangle end up with SOME kind of rational explanation that makes them seem less supernatural than the readers originally thought.
 * Also semi-inverted in the case of Skypeia, though. As a proponent of the New Era philosophy that denies dreams and romanticism, Bellamy attempts to do this by heckling the Straw Hats for believing in a flying continent, even providing an alternate explanation for why a ship might fall out of the sky. Naturally, he gets proven completely wrong, and while the Skypeian continent may have a "rational" explanation for its existence (in-universe, at least) that doesn't diminish the sense of discovery and adventure.
 * Also, it was made clear that ships have been mysteriously disappearing in the Florian Triangle since long before Thriller Bark.
 * This particular revelation is accompanied by a shot of an enormous shadow with glowing eyes in the fog behind Thriller Bark, something that still gives this troper the creeps to this day.
 * Higurashi no Naku Koro Ni sort of counts.
 * A weirdly inverted version in Umineko no Naku Koro Ni: While the witches and their magic seem to be blatantly real, if Battler can explain all the deaths away as the work of normal humans, he'll Do In The Wizard and Retcon them away.
 * Witch Hunter Robin ends with this, explaining all magical powers to be a result of genetic breeding from the original witch. Which is still really magic at its core, just mixed with science.
 * In a similar vein, Ellis of El Cazador De La Bruja turns out to be the product of a project to genetically engineer witches, but these witch powers are genuinely supernatural in nature. The main characters also meet a psychic girl and a harvest spirit disguised as a deceased writer along their journey, without any "rational" explanation given.
 * In the manga version of Chrono Crusade, demons are However, this doesn't completely explain away their more supernatural powers, and there's still plenty of other magical and supernatural elements that are never explained away with science. The reason why this happened, according to the mangaka at an anime con in Seattle, is that he was criticized during the manga's run for not having the demons be accurate to Christian mythology, so he pulled an Authors Saving Throw. Also, the anime adaptation didn't do this and played the supernatural elements straight the whole way through.
 * In the manga version of Sailor Moon, the moon cats Luna and Artemis, who previously seemed to be just another magical element inherited from the ruined Moon Kingdom, are revealed to be from planet Mau, which seems to explain their ability to talk (and turn human). This being Sailor Moon, there's still plenty of magic behind almost any "aliens" that appear in the story, but it was still a noticeable Retcon -- an earlier side story The Lover of Princess Kaguya (basis for the Sailor Moon S Non Serial Movie) where Luna falls in love with a human man has her lamenting being "just a cat"; while it seems to be implied that the cats can't randomly turn human at will, in this story Luna doesn't seem to be aware that she has a human form and only achieves it because of the Ginzuishou power.
 * Also, the Moon Kingdom was a powerful and unique piece of mythopoeia, and its Senshi were originally almost deities -- their official group title is "Soldiers of the Four Guardian Gods". The last series replaces this with there being Senshi all over the Galaxy. It doesn't provide a scientific explanation, but since it destroys the poetic elements of the story, it counts.
 * Madoka Magica: . Magic is still magic, though, more or less.

Comic Books

 * General comic book example: when DC jump-started the Silver Age by reinventing a number of their once-popular characters, they tended to replace mystical origin stories with scientific ones. For instance, the new Green Lantern got his powers from being a space policeman with an advanced technological weapon, rather than finding a magical lantern. This is probably largely because of the influence of Editor in Chief Julius Schwartz, who was also major editor in the field of prose science fiction.
 * The early 1960s Blue Beetle, Dan Garrett, gained superpowers from a magical beetle-shaped amulet from Ancient Egypt. The amulet recently resurfaced in a storyline revealing that it was actually a long-lost bit of Imported Alien Phlebotinum. Justified in that the alien race behind it, the Reach, have disguised many of their plans and weapons as "magic" so that no one would ask questions, while at the same time doing in wizards that could prove otherwise.
 * Although while the scarab is not itself magical, Garrett did use magic to activate it.
 * Likewise, Hawkman's powers are ever-changing in nature: He's either the reincarnation of an Egyptian Pharaoh, or an alien. Or the reincarnation of an alien pharaoh. For example, the mystic that gave the third/fourth Hawkman his powers was retconned into being a Thanagarian scientist.
 * Likewise, the nature of the "Nth Metal" that gives him his powers keeps changing; from a simple anti-gravity material, to all-purpose Green Rocks, either scientific or magical or even angelic in nature and naturally or artificially originating either from Earth, Thanagar or Heaven. Pick one from each column.
 * There was a period when The Mighty Thor and his fellow Asgardians were actually Sufficiently Advanced Aliens whose exploits inspired Norse mythology, but who weren't actually gods. This has since been completely ignored.
 * The official Marvel explanation is that the Norse gods (and all the other pantheons) are extradimensional aliens (Asgard is in a pocket dimension.) That use magic. And technology.
 * The new film also makes the claim that magic and science are in fact one and the same, and Asgard seems to exist physically in another dimension or region of space.
 * Batman has done his fair share of this, usually pointing out people explicitly trying to use smoke-and-mirrors to appear mystical, or some ancient artifact that was thought to be "cursed" or "enchanted" having a rational explanation, like a rage-demon-possessed mask that actually had a few small poison-tipped spikes that drove the bearer mad. That said, he's also explicitly encountered ghosts, wizards, gods and demons, so it's less a case of "There's no such thing as magic" as "I won't believe it's magic until I prove it one way or the other."

Film

 * Star Wars: The Phantom Menace famously did this to the Force and the abilities of the Jedi and Sith, explaining them as the effect of organelles known as midi-chlorians. The movie itself shows that a person's Force potential can be measured by a simple blood test and midi-chlorian count. The idea that there was some genetic component to Force sensitivity was not new to that movie, with the original trilogy showing it occurring between Luke and Anakin (and implying it for Leia).
 * What many people seemed to miss is that the original explanation for the Force wasn't overwritten either. It's still a mystical energy field that "surrounds us, bounds us, ties the galaxy together", except that now you also need high midi-chlorian to access it. Fans were still pissed.
 * The 2009 film Sherlock Holmes,
 * Highlander II the Quickening claimed that Immortals were aliens from the planet Zeist. The director's cut claimed that they're time-traveling Precursors from the prehistoric past. Either way, there are very good reasons that fans say, "There should have been only one", and why all the Highlander media since has tended to agree.
 * The movie version of Doom removed the demonic origin of the, er, demons and made them alien/mutants instead.
 * As did the licensed books (but in a very different way: in the books, they are psychological bioweapons designed to play on human fears, so they are supposed to look like demons and monsters).
 * Also inverted in books in that while the demons are simply alien bioweapons, once the protagonists actually meet other civilizations, it is revealed that
 * A new series of licensed books based specifically on Doom 3 have averted this so far. The demons are demons.
 * American-made horror movies before 1931's Dracula (and several after) insisted on providing a Scooby Doo-ish "rational explanation" at the end, never mind that some of them featured "supernatural" events which couldn't have been faked by a hoaxer under the circumstances given. Example here.
 * The best example would be The Cabinet Of Doctor Caligari, which had "it's all in the patient's head'' Book Ends attached on the insistence of the movie's producers.
 * The Ten Commandments has a scene, like the Bible example mentioned below, where Ramses tries to explain away the Plagues as natural phenomena. To paraphrase, he tells Moses that red mud seeped into the Nile River, causing the frogs to leave and the cattle drinking from it to sicken and die, whose carcasses rotted, attracting rats and bugs that spread disease. Then there's the matter of burning hail from the sky...
 * It doesn't help that some modern historians suggest similar causes such as a mega dust storm, which would also cause these results.
 * Troy retells The Iliad without any gods or magic. In fact, the film's message scorns mysticism, religion, and superstition. In the beginning, Achilles lampshades when a boy asks if he's really invincible. Achilles responds that if he were, then he wouldn't be bothering with a shield. In the myths, Achilles had only one weak spot, but he also wore armor.
 * Everywhere but his weak spot.
 * ... which he didn't know about.
 * This is more the case because it is a Euhemeristic portrayal of an ancient story, not because the directors scorn mysticism; they go out of their way to leave it vague if Achilles is really invulnerable or his mother is really a nymph. Achilles explicitly states he's seen the gods and was not impressed. The shield is actually a bit of Fridge Logic in the Iliad, where Achilles is injured several times and yet is described as an invulnerable juggernaut.
 * This is the damning part: not only do the writers have no regard for the Greek gods, most of the main characters don't, either.
 * The "invincible everywhere but the heel" aspect of the Achilles legend is never mentioned in The Iliad and is only one variant of the myth in the first place, albeit one that eventually became ubiquitous.
 * If you can get your mind off Mathilda May's assets, Lifeforce (aka "The naked space vampire movie") posits that vampire legends are based on a race of alien Life Energy parasites.
 * In The Dark Knight Saga,
 * House of Dracula sweeps aside the supernatural elements of The Wolfman's curse, gives it a Techno Babble explanation and ultimately cures it.
 * In Ghostbusters, the main characters are scientists who catch ghosts using technology. Although both magic and science exists in Ghostbusters. In one episode of the series, it is shown that in the Ghosts' home dimension magic ust be used instead of science to capture them.
 * Ondine has this as a Twist Ending..

Literature

 * Done somewhat blatantly in the Sword of Truth series and can mainly be ascribed to the Sisters of the Light. In the first few books, magic is described as being one's "gift" and prophecies in-world were very traditionally vague. Once the good Sisters are introduced, they bring along their own descriptions, describing the gift as one's "Han". And beyond the fourth book, the previously well-written and plot-relevant prophecies disappear and are replaced with quantum physics Techno Babble meant to sound more scientific than mystical, going beyond Magic a Is Magic A (this is also, not coincidentally, when the story becomes an Author Tract).
 * At this point, the Evil Sisters also start stealing the "Han" of male wizards and using it for themselves, apparently through the power of.
 * One of HP Lovecraft's signature tropes was describing magical incantations as mathematical formulae, and explaining demons and antediluvian gods as aliens, interdimensional beings, time travelers, or time-traveling aliens. He was a staunch atheist, and this was part of the message of his works.
 * The Atrocity Archives by Charles Stross follows on this point; the secret agency that deals with Eldritch Abominations, the Laundry, was founded after Alan Turing discovered a math equation that simulated magic. A Hand of Glory is described as specific variables that form a complete circuit with an extradimensional source, and the traditional "gaze of the Medusa" turns out to be triggered by a very rare form of brain tumor and.
 * Lovecraft's novella At the Mountains of Madness was a wholesale demystification of his own mythos. It explicitly described Cthulhu as an alien, not a deity, which "The Call of Cthulhu" itself did not do.
 * Standard trope in Soviet-era children's fiction. It was usually coupled with the "religion is the opiate of the people" message.
 * The Warlock In Spite Of Himself has the "witches and warlocks" of the Lost Colony of Gramarye revealed as having inheritable mutations that give them Psychic Powers.
 * Until the fourth or fifth book (it's a long series), when it is revealed.
 * In The Coldfire Trilogy, the magic system actively prevents technology from arising (beliefs and fears are made manifest and honestly, who really believes that their car will start each day?). Except... as it turns out,.
 * Brian Stableford's short story "The Garden of Tantalus" is a whodunnit with the Greek philosopher and supposed magician Appollonius of Tyana as the detective. It retells Philostratus's account of Appollonius exposing a lamia, but in this version he exposes a murderer, and the supernatural aspects were later added by his follower Damis (whose diaries Philostratus claimed to have used) to hide the fact he wasn't told what actually happened.
 * Marion Zimmer Bradley's Darkover. Laran, the setting's word for their magic, is a word for psychic abilities that can be amplified through matrix crystals. Bradley does a good job of showing how most native Darkovans call it sorcery, but those who actually work with it treat it as a science. Although the science behind the psychic abilities boils down to "It's magic but not!"
 * To a lesser degree also her Avalon books and Firebrand (they have some magic and some elements explained by more mundane factors).
 * In an unusual variant, the Lord Darcy mysteries take place in a world where sorcery exists, yet the solution to his cases usually turns out to be non-magical. Indeed, Darcy must often prove the culprit used mundane methods so as to exonerate an innocent magician, thus Doing in The Wizard to save the wizard.
 * In The 13 th Warrior, the monster is just a brutal primitive tribe, but no less dangerous.
 * In the afterword to the softcover edition of the book, they are strongly implied to be the last Neanderthals, so the wizard was already done in.
 * Many books by Richard Matheson do this, including I Am Legend and Hell House.
 * According to the (pretty strange) rules of magic in Gordon R. Dickinson's The Dragon Knight series, this is how technology develops. Magicians invent a new type of magical technique that runs on magical energy and share it amongst each other. If they share it too much, it stops being magical and starts being technology and running without mana. The only way to replenish the world's supply of magic is with new magical techniques: the main character invents the theater and special effects in one book which helps replenish the world's supply of magic.
 * Some of Dean Koontz's works prefer to settle for a paranormal solution over a supernatural one, and The Servants of Twilight is a particularly heavy-handed example. The main character's son is pursued by the followers of a religious fanatic throughout, who's had visions that paint the child as the Antichrist. In the final confrontation,, and this, along with other strange occurrences, lead the mother to think her kid might really be the Antichrist..
 * Ann Radcliffe, a late 18th century Gothic novelist, loved this. Most of her books have a big section in the denouement explaining how each and every seemingly-supernatural element was really just the wind, or trickery, or the drugs you were taking while reading... Well, not that last one. This is especially interesting because the supernatural was a hallmark of the Gothic genre, and Ann Radcliffe was one of its foremost writers.
 * The original Sherlock Holmes stories. Pick any story (or novel) with a seemingly supernatural element and that element will be given a rational explanation by the end. Most obvious example is The Hound Of The Baskervilles.
 * Stephen King has Gerald's Game, which featured a superfluous last chapter that establishes that everything had a rational explanation. Not the usual from King, but that may have been the point.
 * Isaac Asimov does this in his Black Widowers series, especially in "The Obvious Factor" and "The Haunted Cabin". Another short story, "The Cross of Lorraine" features a Lawyer Friendly Cameo of the Amazing Randi, who does this for a living.
 * Played with in the Three Investigators series. Often played straight, but some of the "rational" explanations seem to be extremely far-fetched.
 * Scott Westerfeld does this in Peeps, where vampires, and all of their traits, such as being afraid of sunlight and mirrors and crosses are explained away as parasites affecting brain chemistry. Even vampires turning into bats is explained.
 * Subverted in The Apocalypse Door by James D. Macdonald: Over the course of the novel, the protagonists piece together the evidence that the "demons" they're fighting are the spearhead of an extradimensional alien invasion -- but then, at the end, it's suggested that they really are demons.
 * Justified and inverted at the same time in G.K. Chesterton's Father Brown short stories. At first, something supernatural seems to be going on; in the end, the "ghost-story" phenomena turn out to be this-worldly. However, the crime turns out to turn upon the mysteries of the human heart, treated by Chesterton as far more supernatural and dreadful than any ghost.
 * In the Peter Pan-External Retcon Peter and The Starcatchers series, the stuff we know as "fairy dust" is actually "Starstuff", a highly dangerous Applied Phlebotinum that can do anything. Besides being the creative force behind every genius in Earth's history, Starstuff can make people fly,, and if you survive prolonged exposure.

Live-Action TV

 * Doctor Who has somewhat of a running gag (spanning decades) in that The Doctor refuses to say something is magic, and will have a Techno Babble explanation -- sometimes correct, sometimes flimsy and hinted incorrect.
 * This is well shown by the way that companions occasionally BS their way through Doctor-like explanations without any knowledge at all- and sound EXACTLY like him, ala Rose in Turn Left.
 * This attitude is averted, however, in "The Impossible Planet"/"The Satan Pit", in which an entity claiming to be the literal Satan (or at least, the inspiration for him) appears, and claims to be older than time itself - something the Doctor says to be impossible. At the end of the episode, the Doctor all but admits that he doesn't have an explanation and can't dismiss the entity's claims quite so easily as he normally would.
 * In "Battlefield", he admits that Morgaine's powers are magic, however, and gives Ace an inverse of Clarke's Law. "Any advanced form of magic is indistinguishable from technology." The in-episode explanation is that Morgaine comes from an alternate universe with different physical laws, and apparently magic—or something that we might as well call magic—actually works there.
 * Lampshaded in "The Girl in the Fireplace"--He suggests that the 'windows' are "spatio-temporal hyperlinks." When Mickey asks what that means, the Doctor replies, "No idea. Didn't want to say 'magic door.'"
 * Averted in "Midnight" when no explanation is given as to what the antagonist is, nor is the subject even brought up. It is just something that is attacking them. One of many reasons why this episode more than most is top quality terror.
 * Lampshaded in "A Christmas Carol", when one character says that the fish like singing (It Makes Sense in Context), the Doctor denies this and starts rambling about vibrating ice crystals. The fish seem to dislike this and they bite him.
 * Fans complained about Silver Nemesis when Lady Peineforte's magic worked and was actually called magic. The show did an Authors Saving Throw a few episodes later in The Curse of Fenric, claiming her powers had been derived from a Sufficiently Advanced Alien.
 * Lampshaded by Jackie Tyler in Army of Ghosts, complaining that the Doctor is trying to turn the return of their loved ones as ghosts into something scientific. As always, the Doctor is right,
 * A particularly egregious example takes place in "The Daemons" in which the Doctor and a career witch argue for several minutes as to whether an effect is magical or scientific. Then the Doctor explains that it works exactly how the witch thought it did, but if you know how and why it works then that's science.
 * Subverted in The Shakespeare Code, where the Doctor explains a man's sudden death to the witnesses in the terms of then-popular humoral theory, later clarifying that if he tried to tell them the truth, it would make them think it was witchcraft. When asked by Martha what was the cause in fact, the Doctor replies, "Witchcraft."
 * Subverted in The Second Coming, in which the Son of God really has returned and is performing miracles, one of which is to make a sliver of daylight appear within the confines of a football stadium during night. At one point, one of the main characters meets an academic who is studying the footage of the event, who comments that they could theoretically check local weather patterns to see what day's weather had been transplanted to that night. The main character, an atheist, suggests that this is proof that it's not necessarily a miracle, only for the academic to counter that it's nothing of the kind; regardless of when and where the daylight came from and what scientific terms you couch it in, it's still impossible.
 * The Animal Planet movie Werewolves: Dark Survivors has this in spades, attempting to explain all the myths surrounding werewolves as a derived strain of rabies which causes porphyria and other symptoms, with a few historical tidbits about berserkers for good measure.
 * The format of Jonathan Creek involves him using his experience as an illusionist to solve seemingly impossible or paranormal crimes.
 * An episode of Stargate SG 1 had Daniel attempting to do this with a group of villagers. Every time he tried to tell them that there was no such thing as magic, he would be "beamed up" by an orbiting ship, which did not help his case any.
 * In universe examples/attempts of this happen fairly often as the Tau'ri are always trying to explain to other humans that the Goa'uld/Ori are not gods and the that they wield technology not supernatural powers.
 * A Christmas Episode of Eureka has Taggart attempting to do in the Santa, with chimney-climbing device, matter-shrinking ray (for storing the presents), and flying sleigh complete with holographic reindeer. (Though, according to Jack's telling of the events of the night, he failed, and Santa actually exists in the universe. He could be making it up, but then, Eureka does share the same continuity with Warehouse 13...)
 * Lost teased this for a bit. The show initially lacked sci-fi elements, instead apparently featuring an unseen "monster," supernaturally strong natives, the resurrected dead, polar bears created by a child's mind and a healing power that one character attributed to faith. The next seasons, however, revealed that a scientific initiative lived on the Island. It brought the bears, and fans assumed it was behind the show's other mysteries as well. The walking dead appeared to be an illusion of this monster, who had some sort of relationship with the initiative, the healing properties turned out to be due to an "energy pocket" similar to Uluru in Australia and the natives turned out to be ordinary people who lived in suburban-style homes. Then the show's final seasons flipped this around again. The initiative were revealed to be just a recent chapter in the Island's history (and was itself largely demystified). People really could resurrect on the Island. The monster was a millennia-old man at war with his demigod brother. The source of the healing was a magic light that was also the source of all life and rebirth. The natives turned out to have an older, mystic sect that lived at a temple. Meanwhile, every devotee of science on the show was killed, and the lead's arc was portrayed as a transition from "man of science" to "man of faith."
 * In other words, the show was Zig-Zagging with this Trope from the start and until the final episodes.
 * Joan of Arcadia plays with this (briefly) by suggesting Joan's visions.

Mythology

 * Many depictions of Oedipus (including perhaps the famous Oedipus the King) try to downplay many of the more fantastic elements of the story, most specifically the Sphinx... the in-depth human tragedy seems to lose something by also having a Riddle-Spewing Man-Eating She-Beast going around in the Backstory.
 * In Chariots of the Gods, Erich von Daniken put forth the theory that classical mythology was based on ancient people's encounters with extraterrestrials.
 * This is the premise of the Raëlian movement, which treats the Book of Genesis as a mistranslated account of alien scientists creating life on Earth.

New Media

 * The online novel John Dies At the End has malevolent living shadows, demons, and ghosts, all.
 * This gets subverted hard in the sequel. A Man In Black shows up, and, among other things, he can turn invisible and "sit" in midair as if in an invisible chair. The invisibility trick is just that--it takes years of practice, but there's nothing supernatural about it. The invisible chair? That's magic.
 * Red vs. Blue: Reconstruction: Though they had to do this to resolve the plot hole of  Especially with the serious nature of Reconstruction, and Washington bringing the body count higher and higher.

Other

 * Bionicle started out as a deeply mystical story with biomechanical beings bearing Elemental Powers living a tribal life on a strange Patchwork Map island, based on prophecies told by their legends of the Great Spirit. Later it was explained that their whole culture is the result of a glitch in their AI and the lies told by their elders, the island was formed by a malfunctioning Humongous Mecha who had been put into stasis by a virus, and said robot was their Great Spirit all along, whose mission wasn't to protect them and be their god, but to go on an inter-planetary travel, and they were in fact supposed to keep him running. And the Great Beings, hailed as ultra-powerful figures of legend were actually a bunch of geeks/politicians, blinded by For Science-Rule of Cool far too much. All sorts of other sci-fi-ish elements also found their way into the story, like Alternate Universe-traveling, a mystical star turning out to be a giant booster rocket, as well as more and more techno-terms and expressions. As Word of God put it, Bionicle is a story of people being wrong. Though many fans preferred the original, unique flavor of the story, and feel that the sudden overdose of sci-fi made it too generic.
 * This isn't helped by the fact that the Genre Shift also brought about a ton of Plot Holes and makes one wonder how utterly mad the Great Beings are.

Tabletop Games

 * This trope is played with heavily in Mage: The Ascension. The Technocratic Union is a group of magical scientists who are attempting to do in the wizard, while Traditions are more "wizard-like" and try to do in the scientist. In short, the Technocrats (at their best) push for a scientific, rational worldview and the Traditionalists (again, at their best) push for a mystical, spiritual one. Both of the major factions are, to a great degree, trying to influence human society into accepting their point of view in order to solidify reality with their own vision. The irony in part stems from a serious case of Not So Different and Grey and Grey Morality.
 * In Conspiracy X, psychic phenomena are simply another aspect of physics which mainstream human science still haven't figured out. All humans (excluding extremely rare mutations) are psychic, to a degree (explaining things like "intuition" or "empathy"). "Magic" and most magical creatures are actually also a result of this: the vast majority of humans produce more psychic energy than they use, and the excess "seeps" out of their body to create a sort of psychic background force, the so called "Collective Subconscious" of humanity. "Magic" is the manipulation of this psychic "seepage" to achieve all sorts of effects (the rituals work because enough people subconsciously believe they should), demons and spirits are intelligent manifestations of people's fears, and vampires and werewolves are people who were "infected" by the seepage until they were physically and mentally transformed into subconscious archetypes: "The Stalker" and "The Predator", in this case.
 * Subverted in the Horus Heresy series. At the start of the series the Emperor of Mankind has done this to the entire Imperium, which is devoted to pure science and rationality and has done away with the concept of gods and mysticism entirely. Unfortunately the gods are real, and they are pissed. Much of the series thus far has dealt with how the Imperium is coming to grips with living in a galaxy of horrors.
 * This is done in a more general sense over all: where Warhammer had a "magic" phase of a player's round, 40K had a "psychic" phase. That's right, all magic canonically IS just advanced psychic power pulling in little bits of the Warp which simply don't adhere to our definition of physics. It's still magical, it's just magic that can be explained.

Video Games

 * Wizardry. There's always been a mixture of magic and science fiction in the series, but when Wizardry 8 was finally released after a long time, some fans complained about the inclusion of tech stuff, forgetting it had always been there.
 * Metal Gear Solid 2 (the ultimate king of correcting itself) does this forwards and backwards. Fortune, who has luck based powers, causes every shot fired against her to miss (Hint: Don't stand next to her). It then explains much later that she merely has a "sufficiently advanced" bit of technology (that she didn't know about) which makes her Immune to Bullets. This is demonstrated by the owner of the device shooting her in the chest, proving he controls the device and she is powerless. Shortly after this he tries shooting rockets at her, and she deflects them with her mind. Seems in this case, the wizard was Not Quite Dead.
 * Then there's how she initially survived that shot to the chest. Ocelot aimed for her heart, but due to a congenital defect that only effects 1 in 12,000, her heart is on the other side. In other words, she got lucky.
 * There's actually a logical theory to this. Snake was the main ace in the hole for Ocelot's Gambit Roulette. Snake needed to live but Ocelot needed to keep his cover up to keep the Patriots blinded. He may have somehow reactivated Fortune's abilities in order to keep the charade going.
 * Then there's the character of Vamp, who is to all evidence an actual supernatural vampire. In a milieu with psychics, an immortal woman and a man COVERED IN BEES, this isn't so strange it couldn't be pulled off with sheer chutzpah. In MGS4
 * Canonically, it's a chronological shift. Early villains like The Pain, The Sorrow and Psycho Mantis are actually supernatural, later ones like (maybe) Fortune are technology-based imitations of the supernatural. It ties in to the shift from naturally trained soldiers (such as The Boss or Naked Snake) to the fake ones seen in MGS4.
 * Occurs often in the Wild Arms games, where the villains or Precursors will Techno Babble away magical events. Some of these are justified, and some are ridiculously silly.
 * Used halfway; the Might and Magic universe never attempted to explain away the Magic spells or the elves and such. On the other hand, it is implied that all the Gods are only Sufficiently Advanced Aliens and the demons and devils (called Kreegans by themselves) are also aliens, who invade worlds through meteors (they extinguished the halflings (hobbits) this way). There's a significant amount of lost technology behind every plot. Although, there are also actual demons which look almost identical to said Kreegans. They are only seen in Heroes Chronicles: Conquest of the Underworld.
 * However, there is nothing particularly magical about those, considering that a completely human army can go into the Underworld freely. These demons seem to be nothing more than native species that live in that particular area, while the identical looks can be explained by Heroes Chronicles using the same engine and sprites as Heroes of Might and Magic III.
 * Almost every Professor Layton game. Box that kills people who open it? Time travel? Specter terrorizing a town?
 * Always happens in the Star Ocean games, the natives of a planet will use magical terms to describe a villain or phenomenon. Any alien or member of The Federation who is in the party will have a Techno Babble explanation. The funny thing is how the natives in the party more or less ignore these.
 * So very Egregious in Star Ocean the Second Story, where main-character Claude is well-acquainted with science and technology, and tries to explain certain things away in scientific terms, only to fail miserably. He gets better as time goes on (i.e. he learns to stop questioning everything and just accept that he's not that smart.)
 * The wizard finally gets done in once & for all though in the 3rd game, when it turns out that That the code works outside the game is hand waved by saying that the parents of the protagonists created a special kind of science/magic/code that would make their special powers work outside their VR world. In other words, they cast a spell to make magic work in a world with no magic to make spells work. Star Ocean 3 is  written from the other side.
 * In Grandia II,
 * The Condemned series: The original game suggested that a supernatural force was causing the outbreak of violence, and the main character's own apparent insanity. The sequel revealed that However, this particular killed wizard is replaced by a much larger, much stupider one, so to speak.
 * Averted in The Longest Journey, where Arcadia is a world where magic works with no scientific explanation, while Stark is deprived of magic and runs on science and technology (curiously, magical and technological items work fine in opposite worlds, much to April's advantage). On the other hand, April does in the wizard Klacks with a pocket calculator. Don't know why that worked either.
 * In fact, it was the purpose of the Guardian of the Balance to avert Doing in the Wizard by separating science and magic into different worlds. Magic bled over into Stark and science into Arcadia because the Guardian was missing.
 * As revealed in Dreamfall, after the new Guardian restored the Balance and corrected the flows of magic and science, anything in Stark that was based on magic (Anti Gravity, Faster Than Light Travel, etc.) stopped working, as the laws of physics took over. This also explained why there were so many anti-gravity crashes mentioned in The Longest Journey, as magic is inherently chaotic. On the other hand, in Arcadia, anything more advanced than Middle Ages can only work via Magitek, which includes steam engines and airships of the Azadi Empire.
 * The Stinger at the original ending of Infinity Blade and the bonus content  reveal that the setting is science fiction and not fantasy.
 * In the Golden Ending of The Reconstruction, it is revealed that . Magic is still magic, though. Probably.
 * Actually an effect in the Type Moon verse (Fate Stay Night, Tsukihime etc). As modern science develops more and more, magi gradually lose their powers. There's a reason why Fate Stay Night's Caster can canonically take on every living magi in the modern world and win: she's from the age of gods and miracles, and science hasn't nerfed her magic. This is also why the three remaining true magics are so powerful: they are simply beyond modern science and so haven't been hit by this effect at all. At least one modern magi tried to point this out, but his Jerkass teacher tore the research paper up, saying that only being 'pure blood', as it were, mattered. With a progressive attitude like that, no wonder everything's going to well.
 * Ever since the Temple of Time was introduced in The Legend of Zelda Ocarina of Time, the series has featured Time Travel made possible by magic. In The Legend of Zelda Skyward Sword, the properties of the Temple of Time are revealed to stem from the Timeshift Stones, which the robots of Lanayru Desert dig up. It's not nearly as extreme as other examples on this page, as the properties of the Timeshift Stones are harnessed through Magitek rather than straight-forward tech, and time travel is still possible through purely magical means.
 * Anghel Higure in Hatoful Boyfriend at first appears to be an eccentric Daydream Believer from the Manga Club who claims he's a cheesy JRPG-style Fallen Angel, and then, at the end of his route, we find out that he's actually telling the truth. In the BBL route, it's revealed that Anghel was not actually a fallen angel, but a bird with a mutational ability to induce hallucinations in others when physically agitated. Possibly a parody considering the source material, although not definitively.

Web Comics

 * Unicorn Jelly begins as a Dungeons and Dragons-like world with witches who wield magic and fly on brooms, unicorns, elves, ogres, slimes, jellies, and other monsters. Eventually most or all of this gets explained away as being due to a combination of the physics and chemistry of the alien universe, Bizarre Alien Biology, Ancient Conspiracy, Schizo Tech, selective breeding and mutation, and hallucinogenic plants.
 * Tales of the Questor starts off using the word "Lux" as just the Racconans' technical term for their medieval-era world's Force Magic version of Functional Magic, complete with constant uses of terms like "spells," "magic," and "wizard." After over a hundred pages of this, the fundamentalist Christian author devoted a text-heavy side arc to explaining that the force that looked like magic, acted like magic, sparkled like magic, was treated like magic, and frequently called magic wasn't really magic. Another side arc, much later in the comic's run, went further and showed the tragic consequences of Racconans referring to their magic-like powers as magic, implying that they weren't even going to use magic-related terminology anymore. The setting is a heavily researched fantasy setting with orcs, trolls, centaurs, elves, etc etc. Racconans are unique in that all of them can see the ebb and flow of the magical energy they call "lux". Most of them can perform mundane tricks like lighting candles and levitating water, and once in a while one has enough talent to be called a wizard. However, magical aptitude is extremely rare among humans, and most of the humans who claim to be wizards are charlatans or worse. Most false wizards claim that they get their power from gods or devils (and lux just doesn't work that way, which is why Racconans debate the use of the words "wizard" and "magic".) A human who is born with the ability to channel lux will have no idea how to control his power without proper training, and is a danger to everyone around him. This makes most races very afraid of Racconans, because they associate them with human wizardry.
 * Gunnerkrigg Court did it partially with the magic used by Court teachers: magic.
 * Magic is also sometimes called the "etheric sciences". The conflict between technology and nature is actually a fairly big part of the series' cosmology and plot. Attempts by sciencey types to Do In The Wizard are what caused the general area of the Court to be split into the Court (science) and Gillitie Wood (nature), and the Annan Waters to be dug to keep the two seperate; though many on either side would like to believe the other entirely unnecessary, the bridge across the Annan Waters and the position of medium within the Court are acknowledgements that they're not mutually exclusive.
 * El Goonish Shive falls somewhere between this and Magic a Is Magic A. While magic is an accepted and integral part of that universe, Tedd's transformation technology (which was given to him by aliens) as well as Grace's own transformation abilities are said to be more scientific in nature (although they do rely on an alternate form of magic energy to function, to the point where they give a false positive to any magic sensing devices). The way it works is so complicated that it took an arc to explain.
 * Though it's not like magic and inner demons weren't called in the first three months. Look! It's a demonic duck of some sort!
 * In a way, this strip, and the following one, do in the wizard. Though not in the usual way.
 * In an early Full Frontal Nerdity strip, the players in Frank's most recent campaign discover that the 'origin of magic' is acually Sufficiently Advanced Technology and that benevolent aliens are responsible for channeling these 'miracles' to humans. They react much as expected.
 * A later strip some eight years later implies all the campaigns end that way.
 * Errant Story does this in a Wham Episode late in the comic. The whole setting changes in one page from High Fantasy to Science Fiction.
 * Homestuck has this subverted. A functionally omniscient character says there is no such thing as magic, but there are such things as unexplainable technology, superpowers, gods, and quasi-magical pure forces of the multiverse. Several characters continue to refer to their powers as spells anyways. So the wizard was done in but might as well still be around.
 * A rather long Running Gag in MS Paint Adventures was pumpkins disappearing, usually accompanied by some form of the phrase, "What pumpkin?" In Act 6 of Homestuck, it's revealed that the cause behind Jade's disappearing pumpkins was mostly caused by.
 * It's later mentioned by  that pumpkins are somehow unhinged from spacetime, and as such, are easier to teleport than anything else. Which is somewhat understandable: in Homestuck, all teleporting devices are built with failsafes to prevent time paradoxes, and pumpkins aren't destined for much.
 * Wayward Sons: The greek gods weren't gods, they were superpowered aliens.

Web Originals

 * The Salvation War is all about this: Heaven and Hell being actual dimensions, Yahweh ("God") and Satan being actual beings, and angels and demons (including nagas, succubi, and harpies) being real, complete with 'powers'. However, these powers can be and are (at least with the demons) perceived, analyzed, (sometimes) understood... and countered. In the case of Hell's demons, anyway. Although a number of angels were killed in Armageddon, there is still far less information to analyze as of yet both in and out of universe.
 * Shandala, the heroine of Urban Fantasy series Broken Saints, has a variety of Psychic Powers, most notably healing wounds with a touch and unleashing loads of Mind Rape on hostile persons, courtesy of her perpetual hyper-empathic state. In the Grand Finale, it is revealed that
 * Conservapedia has taken it into its collective head that Jesus curing a man's son at the same instant it's asked of him disproves relativity's "action at a distance" rule, and therefore relativity itself. What they fail to realize is that Jesus doing something which supercedes physical laws is an innate part of the "miracleness" of the action. There's also the fact that the time it took for Jesus to say the word decreeing the servant's healing was longer than it would take a light beam to travel from Him to where the servant lay, so there is no conflict with relativity anyway.

Western Animation
"(After finding "robot ghosts")
 * In Venture Bros., Dr. Venture challenges Dr. Orpheus, saying "anything you can do with magic, I can do with science." Hilarity Ensues.
 * In Pirates of the Sargasso, they need Dr. Orpheus's help to deal with a ghost... but before he can finish, Brock simply knocks its head off.
 * Inverted in Dexter's Laboratory episode "Filet of Soul," where Dee-Dee's goldfish dies and causes a "Poltergeist" type of havoc on Dee-Dee; meanwhile Dexter doesn't find a scientific means to control it, like he normally does with all such things.
 * Ben 10 Alien Force. Gwen's magical powers are explained as alien powers inherited from her alien grandmother. The episode in which this revelation is made clear goes on to say that there is no such thing as magic. This despite on a previous episode Gwen clearly used divination to locate their enemies and in the former series Ben 10 there were spells read from incantations, a fountain of youth, and soul-swapping. Oh, and what powers Gwen's powers according to the same episode? Mana. Very much a Voodoo Shark.
 * Then Word of God claims that both Hex and Charmcaster are in fact magic users. Maybe coming from another dimension has something to do with it.....
 * Ben 10 Ultimate Alien makes it plain that "magic" and "mana" are just two different terms for the same thing. Gwen's half-Anodite heritage just makes her really good at it, but its entirely possible for humans like Charmcaster and her people to use it too, with a bit more effort.
 * Played with in one episode of Batman Beyond. Terry recounts the rumors from his high school that a ghost is haunting it to Bruce, expecting him to reply that there's probably a rational explanation to it, because there's no such thing as ghosts. Bruce turns around and says he's met ghosts, demons, wizards, and aliens. He doesn't believe this case, he says, because it sounds too "high school". Terry eventually discovers that it's not a ghost behind the bizarre happenings, but rather a telekinetic teenager who essentially got his powers when a remote control short-circuited.
 * The Flight of Dragons, where the main character got his mind stuck in a dragon and received a lecture about dragon-ness from an older one, upon which he deduced the dragon abilities of flight and firebreathing as possible due to hollow bones, empty spaces in the body for holding gas, and eating limestone (calcium carbonate) - which mixed with stomach acid (hydrochloric acid) produces hydrogen gas that is lighter than air, and ignitable with a spark from the scaly dragon tongue/roof of mouth.
 * Unfortunately, hydrochloric acid actually reacts with limestone to produce carbon dioxide gas (and calcium chloride and water). It is possible to produce hydrogen gas by reacting various acids with with various metals (i.e. not metal compounds or ores) which might have been what the writers were thinking of. Unless, that's how chemistry works in that world.
 * Later, the main character does in a wizard by saying random science words at him.
 * Flight of Dragons is Inspired By The Dragon Knight, under Literature above (and credits the books accordingly). That's why they have the same themes.
 * Every episode of Scooby Doo ends this way, with the ghost turning out to be Old Man Edgars in a rubber mask. This trope is often subverted, however, in such movies as the Loch Ness Monster or the Cajun zombies (don't ask). In the latter the zombies and ghosts were all real, and in the former, though the shenanigans were the typical Scooby Doo villain, the ending implied that yes, there is a monster living in Loch Ness.
 * The premise of Scooby-Doo On Zombie Island is that the gang goes searching to find just one haunting that is actually genuine, and they finally succeed; it feels justified because it acknowledges that all the previous hauntings have been fake. However, some of the 70's and 80's incarnations of the show had real ghosts all the time, most notably The 13 Ghosts of Scooby-Doo, and many fans would say that this was Completely Missing the Point of the show.
 * Futurama does this very frequently, including "Robot Hell", evil Robot Santa with aliens for elves, etc.

Farnsworth: Just as I suspected. These robots were buried in improperly shielded coffins. Their programming leaked into the castle's wiring through this old, abandoned modem, allowing them to project themselves as holograms.

Hermes: Of course! It was so obvious!

Farnsworth: Yes, that sequence of words I said makes perfect sense."


 * In Beast Wars, Starscream's "ghost" from Generation 1 is explained as an almost indestructible Spark.
 * The Maximals, of all "people", try to re-create the accident that made it indestructible and end up with Protoform X (AKA Rampage), a large pissed-off bot who likes to destroy things. In fact, the experiment fails, as.
 * The Simpsons underwent a reverse form of this, starting out a reasonably realistic depiction of late 1980s/early 1990s American working-class life (with only a few farcical touches) and gradually becoming a more "conventional" cartoon where anything could happen. The annual "Treehouse of Horror" Halloween specials (the first one airing in 1990, which was still quite early in the show's run) were arguably started as a way to bring in fantasy and science-fiction elements for one night at a time when the show didn't allow them otherwise.
 * Transformers Animated plays with this. While the AllSpark is shown to have an almost supernatural appearance, Word of God states that it operates on scientific principles (albeit principles neither human or Transformer has cracked). The Magnus Hammer is also given a vague origin. Primus exists as a god, but not many Cybertronians believe in him, save for the Church of Primus. Word of God states that older Cybertronians were primitive, and took billions of years to reach their current level of technology. Exactly who their creators are is a mystery, but it is heavily implied that they were Sufficiently Advanced Aliens that modeled Cybertron and its inhabitants (including beast-type robots) after their own world. Additionally, there are no Thirteen Primes in Transformers. Derrick Wyatt has also revealed on Formspring that the inner workings of Cybertron contain a "giant robot factory."
 * An episode of Family Guy revealed that Rudolph's shiny red nose was the result of a brain tumor-induced mutation that would eventually kill him.

Real Life

 * Some famous magicians, such as James Randi, and Penn&Teller's Bullshit!, specialize in debunking mysticisms with scientific explanations.
 * Houdini debunked seances posthumously. Prior to his death, he told his wife a secret phrase that he would use if there was an afterlife and she would try to call him through a seance. Since that secret phrase never cropped up in any of the seances where his wife tried to summon him... well...
 * From the opposite point of view, revealing the secrets of magic tricks.
 * The scientific method has done in a small army of wizards, djinn, dragons, and the like. For example, death certificates from pre-scientific England list such causes of death as comet, the king's evil (a real disease, but one thought to be specially curable by the touch of a king), and sorcery.
 * Inverted by the News in examples like dynamic camouflage (a surface that changes what it looks like to match whatever is behind it), which is framed universally as a magical Harry Potter-esque Invisibility Cloak.