JoJo's 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 Polnareff 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 example 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 imminent Mykene invasion. It turns out that in reality he was Prof. Kenzo Kabuto, father of Kouji and Shiro, who knew about the Mykene due to reasons have nothing to do with prophecies.
And in the episode 36 of Mazinger Z, Baron Ashura pretended being a witch.
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.
To date, there is exactly one supernatural occurrence that has not been given a logical or scientific explanation in-universe: The Klabautermann. It's described as a spirit that is attracted to a well-loved ship, such as the Straw Hats' Going Merry, manifesting when a ship nears the ends of its life. It's used to explain how the Merry was mysteriously repaired overnight during the Skypeia arc, but no explanation is given for the spirit itself beyond the legend.
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 really aliens who crash-landed in the Atlantic Ocean and are now living underwater in their mothership. So a lot of what seems 'magical' about them is really Bizarre Alien Biology or extremely advanced technology. 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 Author's 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 SNon-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.
Puella Magi Madoka Magica: Kyubey is a Sufficiently Advanced Alien, not a magical creature, and he wants to prevent the universe's heat death by breaking the second law of thermodynamics. However, he does this by performing genuine miracles and drawing out real magical potential in human girls so he can collect energy generated by emotions; none of these are governed by thermodynamics or any kind of science and that's why they suit Kyubey's purpose. A rare case of also counting as Doing in the Scientist.
The Second Hokage in Naruto calmly explains the actual process of causing a Sharingan to evolve. Whereas the standard method known for developing the Mangekyo is "kill your best friend", he explains that during moments of severe emotional anguish, the Uchiha's brain releases a special chakra that mutates their eyes.
When Dragon Ball gave way to Dragon Ball Z, the stories took on more of a sci-fi tone. Goku's previously inexplicable talents (and his tail) were retconned as the product of his alien biology. His tendency to transform into a giant monster under the full moon was given a delightfully preposterous "explanation" in terms of electromagnetic waves and hormones. Even Kami, who was for all practical purposes a god, was demoted to a strange visitor from yet another planet. Nevertheless, there were still plenty of fantasy elements, and the sci-fi aspect was downplayed in later stories.
Young Beichan is what is called a "rationalized" version of a fairy tale where the daughter of the witch/ogre/other magical evil helps the hero flee; she's the daughter of an evil king.
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 later 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 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. Agents of S.H.I.E.L.D. reiterates this, stating that Asgardians are just Sufficiently Advanced Aliens that early Europeans thought were supernatural beings. A character even claims that a Norse artifact was brought down from the heavens, at which point Agent Coulson corrects him and says it was brought down by aliens.
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."
In Ultimate Marvel the origin of mutants powers was retooled as something that was scientifically made. Super Serum instead of an evolution process.
In mainstream Marvel it's been canon for a long time that mutants are the product of the Eternals messing with the human evolutionary process, and isn't natural.
The mainstream version of Black Knight is a mystical knight with an enchanted sword from the time of King Arthur. The Ultimate Black Knight is a quadriplegic Cyborg with Artificial Limbs and a suit of Powered Armor.
This is true of a lot of characters, since the Ultimate Universe is generally lighter on magic and mysticism than the mainstream Marvel Universe. A good example is that Hawkeye refuses to believe Ghost Rider is actually from Hell, and instead thinks he's just a mutant who happens to have a flaming skull.
Valkyrie from The Ultimates started off this way (she was just a Thor Fangirl rather than an actual Norse deity), but ended up being given magical powers by Loki.
Ultimate Captain Britain was just a guy in a superpowered costume, unlike the mainstream Captain Britain, who was actually granted magical powers by Merlin.
In Ultimate Spider-Man, the Venom symbiote is a life-form created by Peter and Eddie Brock's dad in an attempt to cure cancer, rather than an alien life-form.
Subverted by Thor, however. The Ultimate version of him often teased that he wasn't really a deity, leaving conflicting hints that he was actually just a man with super-powers that suffered a mental breakdown and was now under the delusion he was a Norse God. Then revealed that he's a deity after all and all the hints to otherwise were planted by Loki to fuck with him.
Officially, Mephisto is not literally the devil in Marvel's comics; he just gets off on convincing people that he is. Magic is a very real, very prominent force in Marvel stories...sometimes. Depending on the writer and the tone of the series, seemingly magical elements may be written off as fantastic technology and demons may in fact be interdimensional aliens...or not. It's all quite confusing, really, but the go-to solution seems to be simply not to worry about it too much.
The Writing On The Wall has Adventurer Archaeologist Daring Do working on excavating an ancient, imposing building constructed deep in the desert. Daring Do dismisses the metallic thorns constructed around the ediface as something meant to deter tomb robbers, and the eponymous writing inside the building as an attempt to scare people away with a nonexistent curse on anyone who disturbed the sanctity of the place. Too bad she was Wrong Genre Savvy and Right for the Wrong Reasons; the words and the thorns were both meant to deter tomb robbers, but the building isn't a tomb, and the "curse" was a warning of the very real, but entirely non-magical danger which lay within.
One of the appendices to Act II of the My Little Pony: Friendship Is Magic alternate continuity Legends of Equestria models magic as an imperative programming language, composed of elementary instructions that unicorns have over time abstracted into personal "libraries" that allow them to cast more complicated spells with less effort. It even points out that magic is almost-provably Turing complete under this model.
Frigid Winds And Burning Hearts effectively destroys most of the magic of Equestria. The Everfree Forest is just a nature preserve (it even has poachers), Discord is just a mundane tyrant, the retelling of Equestria's founding doesn't have Windigoes, and almost everything out of the ordinary is because of deliberate meddling, not because of any magical nature of the place. Even "The Stare" is just something that ponies who work with animals learn!
While generally inverted in Diaries of a Madman, the elementals are actually a race comprised of nanomachines, rather than beings of magic.
Kitsune no Ken: Fist of the Fox is set in a High School AU setting, and as such it's made clear from the outset that there won't be any ninja jutsu, summoning magic, bloodline abilities, or any of the Bijuu present in the story.
Star Wars: The Phantom Menace famously did this to Force ability. In the original trilogy, Force potential is vague, but could be passed down through the family and sensed by other Jedi. The Phantom Menace reveals that a person's ability to control the Force is determined by the amount of symbiotic organisms known as midi-chlorians in the bloodstream. Thus, Force potential becomes solidified as a physical property of your body rather than an abstract talent or metaphysical ability. The Force itself is still just magic, however.
The Ten Commandments has a scene 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...
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 it when a boy asks if he's really invincible. Achilles responds that if he were, then he wouldn't be bothering with a shield.
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.
Ra's Al-Ghul is not ageless and there are no Lazarus Pits: instead, the League of Shadows makes him appear ageless via a legacy of similar-looking figureheads, while the real head and The Dragon really have their places switched every time. It applies elsewhere in the saga as well:
The Joker is... an interesting case. We don't know how much of his backstory has changed because we don't know what his new backstory actually is (or, for that matter, what his canonical old backstory actually was ... the problem is less that we don't have one than that we don't have one; the several stories that Joker tells in the film lampshade this, in a way). While it's entirely possible that he still fell into a vat of toxic chemicals, it didn't bleach his skin or hair; he merely wears clown makeup over a Glasgow Grin (of unknown origins), and said makeup appears to be for possible psychological purposes (a Mook compares it to warpaint).
Two-Face doesn't have dual personalities fighting for control and uses a coin to decide, but is instead a man driven mad with grief and rage and views chance as the only true morality.
Bane's chemical compound is still fed to his body through tubes, but they don't call it Venom and it doesn't make him stronger; he just really is that strong. Instead the mask's chemicals are some sort of anesthetic gas to cope with extreme physical pain.
Ondine has this as a Twist Ending. Ondine isn't really a selkie, just a really good swimmer. The "seal coat" is actually smuggled drugs, the "selkie husband" is a drug baron, her mystical song is actually a foreign pop song and that also means that Annie getting a replacement kidney is just pure coincidence.
In Thor, what would appear at first to be flat out magic used by what appear to be Norse gods, it is shown that they are actually just a shockingly human looking race of aliens from a distant planet, with technology so advanced that it appears as magic to Humans, and the Norse mythology was sprung from centuries ago when they visited Earth and people thought they were gods. A mixed example; Thor's hammer and Loki's magic are both explicitly called magic by Asgardians. Then again, that is how Norse mythology had explained it. After all, who's to say modern people aren't mistaking magic for science?
The protagonist of The Illusionist abandons his illusions for seances and shows wherein he seems to actually communicate with the dead. Turns out he's just a really, REALLY good illusionist... I guess the title should have given it away.
In X-Men: The Last Stand, The Juggernaut never has his origin given, and is at least believed by the populace to be just another mutant. In the comics, he gets his powers and armor from a mystical gem. The Phoenix is just Jean Grey's alternate personality, rather than a god-like cosmic entity. Though to be fair, the Phoenix originally was just Jean in the comics before it was Retconned into being a creature from space.
Played with in Hellraiser Hell World. The Lament Configuration? An online puzzle. Pinhead? Literally called a franchise icon. Hellworld? An exclusive, debauched party. It's all just a game, until things get real and cenobites start showing up and the bloodbath begins. Then the wizard is done in a second time, as it's all the means a mundane killer uses to pick off the protagonists after drugging them with hallucinogens so they'd see what he put in their heads. Then, the wizard rises from the grave to kill the scientist, as the original killer opens the Lament Configuration and the franchise icon puts in his obligatory appearance.
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 physicstechnobabble 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 spiky demon penis.
One of H.P. 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 can be replicated on a circuit board.
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.
Legend has it that Abdul Alhazred, the Mad Arab, was killed in broad daylight by an invisible monster. Most mythos material that draws stictly from Lovecraft runs with this, but August Derleth later expanded on it, explaining that that whole thing was simply a hoax to cover up his even more painful death by torture.
Lovecraft's story "The Dreams in the Witch-House" starts with the protagonist moving into the titular building because his curiosity is aroused by rumors that it is haunted by the ghost of the witch who once lived there. In a way it is, but it is heavily implied that the "haunting" is not actually supernatural but an extremely sophisticated science based around the manipulation of space and time.
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 the main character is an actual magic user, not a psychic. Except that it's then (later in the same book) revealed that he is a psychic. The reason he can use 'actual magic' earlier in the book is that he's been transported to an alternate universe where there is actual magic. Once he gets back home, he can't do magic, but he keeps the psychic powers that he's now unlocked. (Hence the title of this book - The Warlock Unlocked.
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, the inhabitants of the planet are descendants of earlier space travelers, and the "magic" is the result of injured psychic aliens.
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 and is very explicitly treated as a science; Darcy's associate Master Sean O'Lochlainn mentions that one of the reasons he has an M.S. (Master of Sorcery) degree rather than the Th.D. (Thaumaturgae Doctoralis) is that he "couldn't handle the math" required for the latter. However, 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 13th Warrior, the monster is actually a brutal primitive tribe, implied to be the last Neanderthals.
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, the fanatic is attacked and killed by a horde of bats, and this, along with other strange occurrences, lead the mother to think her kid might really be the Antichrist. And that's when the fanatic's top mook — who has been mostly silent throughout and shown no signs of higher thinking — goes into a two-page explanation about how the two characters were most likely psychic and picking up on one another, before walking out of the book entirely.
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.
Black Castle Olshansky mystery novel by Vladimir Korotkevich has in-universe example. Everyone, and the protagonist himself, feels nothing but frustration when the protagonist finds the scientific explanation of the haunting in the titular black castle.
Caleb Carr's The Legend of Broken mostly plays this straight. The "sorcerer" Caliphestos is just a scholar, healer and proto-scientist (and hates being called a sorcerer) and the Bane a tribe of goblin-elves is the product of inbreeding among people exiled for not matching up the the physical standards of the City-state of Broken. However it's hinted that the lost manuscript on which the story is based was written by Broken's founder based on dream visions and Caliphestos has a seemingly supernatural rapport with the pantheress Stasi that's never really explained.
Anne McCaffrey's Dragonriders of Pern series begins with fire-breathing dragons, telepathy, and teleportation, all believed to be a form of magic. By the third book in the series, the dragons are genetically modified lizards with technobabble explanations for the telepathy and teleportation and telekinesis that let the massive dragons fly with wings too small for their bodies.
The Doom series changes the video game's demons from hell into genetically engineered alien monsters. They were created to resemble demons because the aliens had last reconnoitered Earth during The Middle Ages. Fly was raised Roman Catholic and knows that man-made weapons shouldn't be able to destroy real demons. Some monsters have organic weaponry and others have cybernetic weapons installed.
Sergey Lukyanenko's Rough Draft duology has the protagonist become into a superhuman being called a "functional", meeting other functionals with supernatural abilities. While parallel worlds are key to the duology, the nature of these powers are kept ambiguous for much of it. It's clear that someone is behind all this, but how this is done is not described. However, shortly before the end of the second novel, the protagonist claims that all this has to do with advanced knowledge of quantum physics. Why do functionals have these abilities? They "borrow" them from a parallel version of themselves that exists in a world where this is natural.
Doctor Who has somewhat of a running gag (spanning decades) in that The Doctor refuses to say something is magic, and will have a technobabble explanation — sometimes correct, sometimes flimsy and hinted incorrect. However, it should be noted that psychic powers do factually exist in the universe of Doctor Who.
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, à la 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.'"
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.
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, the "ghosts" are Cybermen forcing their way into our universe from another.
A particularly egregious example takes place in "The Dæmons" 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." Though then explained as an alternate form of science which uses the power of spoken language rather than mathematics to operate. Therefore, the pseudo-Shakespearean speech of the witches is in fact their version of technology.
In the Star Trek: The Next Generation episode "Devil's Due", a planet made a supposed deal with the Devil to save their planet. The TNG crew basically does this when a con woman assumes the role of "Ardra" (that planet's Satan) and uses high technology to emulate the prophecies.
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, Eurekadoes share the same continuity with Warehouse 13…) Taggart was actually attempting to prove that Santa DOES exist…or could, anyway. More like Justifying the Wizard.
LOST: Deliberately averted. Damon Lindelof, a noted Star Wars fan, explicitly wanted to avoid either a Midiclorian situation or an Architect scene (which he described as the worst scene in all of sci-fi). So he wrote a show where everybody has their own personal convictions about what's going on with life, the universe, and everything, and then stubbornly argue about it for six seasons. Some people believe in magic and spirituality guiding their lives, whereas others insist they make their own luck and try to do in the wizard with science. Both sides are shown to be right and wrong at times, with evidence to support both their claims, but everything is vague enough that there's no concrete answer, zig-zagging this trope from first episode to last.
Joan of Arcadia plays with this (briefly) by suggesting Joan's visions could be due to Lyme's disease.
The show's version of Solomon Grundy is a normal guy who becomes mutated by a Super Serum. In the comics, he was a zombie who was resurrected by supernatural means.
One episode of House featured a teenage faith healer who apparently sent another patient's cancer into remission with a touch. Only to turn out that he gave her Herpes that attacked the cancer, he'd been picking at his sores before he touched her.
Another episode featured a doubting priest who began having visions of Jesus, stigmata, and other "prophetic" style symptoms. Eventually, House proved all the physical signs were merely the symptoms of a disease. The visions he figured were just alcohol-induced.
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.
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.
Also the premise of Scientology, and all three are proof that this does not always produce a more plausible—or less silly—explanation.
The online novel John Dies at the End has malevolent living shadows, demons, and ghosts, all actually the product of hostile extradimensional biotechnology.
This gets subverted 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: There's no such thing as ghosts. Church and Tex are AI programs. Though they had to do this to resolve the plot hole of Church and Tex coming back, but everybody else stays down when killed. Especially with the serious nature of Reconstruction, and Washington bringing the body count higher and higher.
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.
In fairness, many of these things were not a retcon — the Great Spirit Mata Nui was always meant to be a giant robot that the Matoran inhabited, and the Red Star was always supposed to be a mothership of some sort. The story was just much more subtle about its sci-fi elements towards the beginning. It's a clever bit of in-universe application of Clarke'sThirdLaw.
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.
BattleTech did in its sole canonical mystical element, the PhantomMech ability, with Word of God stating that there isn't really a supernatural ability to evade fire that only affects the Kells, but rather a powerful Lostech ECM package that the Kells have very much not told anyone about. While this raises several questions, particularly in regard to the way certain battles were known to have progressed, this, as well as the decision to ignore the sole canonical instance of sapient aliens in the setting, have firmly established the Battletech universe as one where technology, not mysticism, is a central tenet.
Metal Gear Solid 2: Sons of Liberty (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. note She is also revealed to have survived the aforementioned chest wound because of a rare birth defect that put her heart on the right side of her body, suggesting that her luck-based abilities sometimes work in more subtle ways. Seems in this case, the wizard was Not Quite Dead.
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.
Unless he was outright lying which in the case of a man bleeding to death and questioning the believes that defined his horrible life is rather unlikely, Psycho Mantis was an actual telepath who developed psychic on his own and kept it hidden for years before he was discovered by soviet scientists. Also Vulcan Raven seemed to have actual magic powers. While it's very hard to tell what things are magic and which are not (as pretty much everything that happens in the games could possibly be a deception), the evidence strongly suggests that there is some kind of magic that exists, which is often enhanced by technology.
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 MGS4we find out his healing abilities are natural... but augmented by nanomachines. His fighting and knife skills are Charles Atlas Superpowers... but the rest is technology.
Metal Gear Solid, at least by the fourth game, is pretty consistent with respect to there being both magic (or, at least, very peculiar abilities obtained through training and practice) and technology. Most nanomachine based abilities either enhance innate abilities (Psycho Mantis and Vamp being the most blatant examples, as both have innate abilities that are cranked up to 11 by the nanomachines) or are abilities that have been studied or cultivated and passed on through nanomachines (Screaming Mantis). And pretty much every particularly questionable point can be summed up with the mantra ``Ocelot is a Dick who is screwing with us''
Occurs often in the Wild ARMs games, where the villains or Precursors will Technobabble 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? Hallucinogenic gas. Time travel? Massive underground cavern and a house that's really an elevator down. Specter terrorizing a town? Excavation robot and a giant prehistoric manatee fighting. No, seriously.
Though, to be fair, there is actual time travel revealed after the one they thought was real proved to be fake. It's flawed, but it's real.
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 technobabble explanation. The funny thing is how the natives in the party more or less ignore these.
So veryegregious 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 their entire universe is a computer game & the "magic" is just computer code that temporarily overwrites the physics engine. 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 A.I. Is a Crapshoot written from the other side.
In Grandia II, the gods Granas and Valmar were originally scientists who made what could only described as an ascension-to-godhood machine.
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 it was a cult which was using sonic technology to drive people mad by causing hemorrhaging in the brain. 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: The Longest Journey, 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 AzadiEmpire.
The Stinger at the original ending of Infinity Bladein which the Warrior activates the God King's iPhone and brings up a holographic display of Earth and the bonus content in which the Warrior faces a clone of his Ancestor that is piloting a Mini-Mecha in the God King's cloning facility reveal that the setting is science fiction and not fantasy.
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.
It's more complicated than that, since the time travel in Ocarina of Time is explicitly referred to as a property of the Master Sword, not the Temple itself. There are just several ways to travel through time in the series, the Timeshift stones being one of them, but not the only one.
In Quantum Conundrum, you can shift to a dimension where everything falls up. Professor Quadwrangle jokes about the possibility that, instead of shifting to a dimension where the laws of gravity are inverted, you simply shift to a dimension where the mansion is upside down.
A weirdly inverted version in Umineko: When They Cry: 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. While it's never outright stated whether everything is magic or mundane, it's still eventually made clear that from a mundane perspective, the "magical" characters aren't real at all; they're either meant to be symbolic or the product of a human character's imagination. There's also "Our Confession", a side material that shows how Yasu used trickery and bribery to commit the murders.
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. However, he does also know things he should not be able to know, and then there's what happens in his story in Holiday Star, making it lean towards of Maybe Magic, Maybe Mundane.
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 luxwill 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: They get it by using a computer... Itself powered by 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 separate; 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.
Errant Story does this in a Wham Episode late in the comic. It's revealed in an Apocalyptic Log-style expository page that the Elven Creator Gods were actually Sufficiently Advanced Aliens whose entire species had coalesced into three "collectives" - superpowered Energy Beings. After one of them died/disappeared and the others began to destabilize, they made the Paedagogusi, Dwarves, Elves and Trolls in a failed attempt to create a replacement collective and restore their stability. 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 Jake English fooling around with his transmaterializer too much.
It's later mentioned by Roxy 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.
Spoofed in an arc of Schlock Mercenary involving a "haunted" spaceship. There proves to be a scientific explanation, but it's actually profoundly less likely than the ship simply being haunted, to the point that the ship's AI actually went insane trying to figure out how it could possibly happen.
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.
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.note And even ignoring that, the argument is inherently silly for putting far more faith in both the accuracy of first century timepieces and the precision of speech of first-century people with respect to precise chronology than could possibly be warranted.
Funny Business is about a girl who can basically do anything. For the first half, this is treated as something akin to magic, but in the second half, a quasi-scientific explanation is offered; namely, that the whole setting is just a computer simulation, so the main character can do impossible things like in a lucid dream, and every other character is just a figment of her mind.
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 - Anodites are Energy Beingsmade of the stuff - but its entirely possible for humans like Charmcaster and her people to use it too, with a bit more effort. Around the time we start delving into this, spellbooks and such make their return. (There's a really interesting battle between Gwen and Sunny, a full Anodite, that shows the difference: Sunny's Anodite powers are stronger so she's really tearing the place up with energy blasts and force fields. Gwen's raw power is weaker as she's half human, but the manner of effects she can create through spell-casting is a much wider variety. Ultimately, she just doesn't have the raw power to defeat Sunny, but she holds out long enough for Verdona - their grandmother, a much older and ridiculously strong Anodite - to arrive to put Sunny in her place.)
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 got his powers when a robot's remote control malfunctioned.
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.
Later, the main character does in a wizard by saying random science words at him.
Flight of Dragons is Inspired ByThe Dragon Knight, under Literature above (and credits the books accordingly). That's why they have the same themes.
Also inspired by The Flight of Dragons by Peter Dickinson, a book published three years earlier.
Every episode of Scooby-Doo ends this way, with the ghost turning out to be someone like Old Man Edgars in a rubber mask. Sometimes a two-fold disguise for added punch. 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 Comically Missing the Point of the show. But then again, there is the issue of certain divisive characters causing fans and writers to quietly sweep certain Scooby-Doo series under the rug, which accounts for writer forgetfulness.
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.
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 Rampage's spark is destroyed by Depth Charge.
The spark was shown as not indestructible when Megatron cuts a portion of it out to become the spark for Dinobot II.
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 J Wyatt has also revealed on Formspring that the inner workings of Cybertron contain a "giant robot factory." Of course, a lot of this is writers giving their own, sometimes conflicting interpretation of what they didn't get to make canon, and comes together to get pretty confusing. Transformers is the work of far too many hands to consider anyone "god" enough to give absolute Word of God about how it all works.
The shows themselves have a strange relationship with "the wizard," where things we'd call "magic" are described in sciency terms because, well, they're robots. Gods, demons, Ki Attacks, Psychic Powers, Battle Auras, and The Lifestream all exist, but don't expect them to ever be called that or explained to death in a 'midichlorian' sort of way.
Though even the "not calling it magic" bit isn't always consistent; Transformers Prime, especially, sometimes came within a hair's breadth of stating that certain things were explicitly supernatural.
When it comes to the Allspark in Animated, the writers explicitly mentioned "midichlorians" as the kind of overly complicated and unsatisfying origin they're trying to avoid; where it comes from and how it works gets no mention at all. (This fits with the movies as well: "Before time began, there was... the cube." is all you're getting.)
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.
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.
Some famous magicians, such as James Randi and Penn & Teller, specialize in debunking mysticisms with scientific explanations. Harry Houdini was also interested in debunking mediums of his age. He even established a secret phrase with his wife that he would use if he should die and she should try to contact him through a seance. He did die fairly young and his wife tried for many years after his death to contact him through mediums, who all failed to deliver his secret phrase (except for Arthur Ford who claimed success in 1929, only to be exposed as a faker later... another debunking by Houdini posthumously, so to speak).
Revealing the secrets of sleight-of-hand illusions and such takes the "magic" out of the 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.