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In the Haruhi Suzumiya series, the Data Overmind and its Artificial Human agents use non-mechanical technology that the narrator usually just describes as "magic", since it can directly overwrite reality. As a result, Humanoid Interfaces fighting looks an awful lot like a Magical Girl battle. It's also implied that humanity, in The Future, will use similar technology, which is why the series's representative Time Traveler can't operate any present-day technology more complicated than a flashlight; her society has outgrown such silly things as thermodynamics.
A variant of this is presented in episode 14 of the Umineko: When They Cry anime. Virgillia explains that the Japanese fire ceremony, which today has been explained by science, was once seen as magic because it was like that to people at the time.
Battler: In other words, if you don't know the principles it's based upon, a rain ceremony is just like magic?
Somewhat in the franchise, Digimon. All There in the Manual video games reveal that the two first computers, ENIAC and ABC started the digital world. There's the technology side, and this creates digimon who knows magic, demons and angels, mythical creatures and a Magic Land within the Cyber Space.
Show: Full Metal Panic!. Scene: two Real Robots are fighting with kinetic guns. One of them loses its weapon; the other tries to shoot but the bullet is absorbed by a forcefield that seemingly sprang up from nowhere. The attacker's yelp of surprise is then interrupted by the other guy shooting a giant shockwave of energy from his palm. Another guy complains not a minute ago that while fighting it, his cannon round bounced back and destroyed his own bot even though the opponent clearly doesn't have reactive armor. Say hello to the Lambda Driver with no-one knowing how exactly it works, only that it works... most of the time.
In chapter 42 of Yozakura Quartet, Arthur Clarke's third law is quoted by one of the senate members to Gin/Enjin in regards to Onmyou.
Lupin III has the villain Pycal, who was impervious to bullets and fire, could walk on air, and shoot fire from his fingertips. Lupin found a way to replicate these tricks: (he walked on air via carefully placed glass panes, shot fire from his fingertips with a small, hidden flamethrower and was impervious thanks to a hard liquid chemical that shielded his body when covered by the liquid.) It was never explicitly confirmed that Pycal really wasn't using magic in the manga version, though in the anime Lupin found Pycal's chemical formula. When the villain was revisited in the OVAReturn Of The Magician, he received upgrades in power, and was seeking a collection of crystals that were able to use vibrations/sounds to do whatever he wanted. Naturally, Lupin also has his eyes on them, and the two fight over who gets to collect all of them.
Ghost Sweeper Mikami had an story arc with the mother of Mikami utilizing the power of a nuclear aircraft carrier with a big magic circle drawn on the deck and fighting demons a few hundred times more powerful then herself.
In One Piece, Nami is able to practically control the weather through the use of her knowledge and her staff which can manipulate temperatures in the atmosphere. To the point most people actually mistake her for a witch. Again after the time skip, where she even corrects one of the enemies by stating her abilities is "purely science" while using a new staff she calls "sorcery climate".
The Incubators from Puella Magi Madoka Magica have reached the point where it is impossible for us humans to any longer tell what is "magic" and what is "technology" to them. Like Lovecraft's various aliens, their understanding of physics and the universe is so far beyond our own that they can do things like manipulate souls or give people visions just by looking into their eyes. While still insisting all the way through that for them, this is all strictly science. Strangely, the Incubators still refer to magic as such. To them it's a type of energy created from emotion, which breaks thermodynamics, and is therefore extremely useful.
Yu-Gi-Oh!! and all its sequels use this in every "Shadow Duel" (Yami no game) where the monsters/cards are not merely holograms anymore but are in fact real and fully able to cause damage to the opponent. Even after countless previous encounters with taking real damage from these games, The Protagonist always ends up surprised in their subsequent duels.
A very big point in Cyber Weapon Z where the crossing of magic and technology are used in conjunction in order to build much more effective devices than the usual mechanical stuff.
Shiro Sanada, from Space Battleship Yamato 2199, actually quotes Arthur C. Clarke when discussing how Iscandarian technology seems to defy the laws of physics and nature as we know them.
The Flash villain Abra Kadabra was from a far future time, who used his advanced technology as "magic". Over the decades, this has sometimes been played straight, and sometimes Retconned into either real magic or innate Psychic Powers, and the "technology" as just props used as a psychological crutch. Others split the difference and say it's Magitek. At one point, he sold his soul to Neron for real magic.
Gold Digger both exemplified and subverted this in equal measure.
At one point, Gina discovers that magic is just a derivative of an ancient Magitek known as Beta Technology. The Saurians who were involved in its creation bio-engineered the dragons as a slave race, encoding them with the ability to use magic (how it works) but not the principles of the science (why it works). After the dragons rebelled and the Saurians were mostly wiped out, the knowledge of how everything worked was lost or sealed away, and what little the dragons knew about how things worked combined with the knowledge of other races formed the basis of ancient magic, with technology becoming a different science altogether. This explains why the Artificer, Gina's future identity, is a spellcaster beyond the comprehension of all but the most powerful Big Bad, Dreadwing, and Gina is unable to comprehend even the most basic levitation spell in the present, though bits and pieces of her research that will eventually lead to this revelation have actively worried many magical authorities about Gina's continuing "merging" of magic and technology, which works in ways they don't understand.
However, a later revelation added another layer in that the Magitek that formed the basis of Beta Technology is the physics and science of the previous universe, destroyed before our Big Bang. When survivors of that universe managed to thread the needle and escape into the new universe, they brought their science with them, which bent the natural laws of the new universe in ways that shouldn't be possible, thus making it this and Magitek simultaneously.
Skartaris, the setting for The Warlord, not only contains genuine magic but a lot of pre-cataclysmic Atlantean technology that functions like magic to the primitive inhabitants.
Apparently the Day Of Wonders virtual reality program in the Apocalypse series is so real it can hurt and even kill people who enter into it: a lethal snake bite in the program also becomes a lethal snake bite in reality. Willy Spino in Revelation when he first entered the Day Of Wonders program after it was hacked ran his virtual self fingers on the blade of a guillotine in the program and ended up cutting his finger in reality. It may not be the programming of the Day Of Wonders that causes it to be that real, but actually the power of the Antichrist working within the program itself.
Thor presents the Asgardians as a race whose technology seems magical, or perhaps they have advanced beyond the point where there is a distinction. Also, old Norse legends such as Yggdrasil and the Nine Realms have a cosmological explanation. At one point, Dr. Jane Foster even cited Clarke's law; "Well magic's just science that we don't understand yet; Arthur C. Clarke."
Blackwood in Sherlock Holmes tries to pass himself of as a sorcerer protected by Black Magic; Holmes deduces an explanation for every trick he performs derived from a combination of science and theatrics. Holmes also notes however, that Blackwood has indeed actually performed the dark rituals exactly as they were described in religious texts, so perhaps Blackwood had better hope that none of it was real after all (otherwise, he will have quite a price to pay when the bill on his eternal soul comes due.)
In John Carter, the ancient, immortal Therns wield what a modern man might call weaponized nano- or femtotechnology (powered by the "Ninth Ray"). It takes the form of an easily-concealed mass of lichen-like vines that grow and adapt to the user's needs: making beam weapons of various sizes, Absurdly Sharp Blades, and even crawling on the skin of someone else to either kill them by crushing the skull or restrain their movement by implanting themselves into the skin. Of course, since this is the very early 20th century, the stuff looks more like magic than anything. Other powers include a means of Voluntary Shapeshifting, long-range communication and travel and a medallion that can transport people between planets via Astral Projection (that is, leaving the original body sleeping where you left it, and sending a copy with your mind in it to the destination).
Not quite as deeply involved, but Lex Luthor said the page quote in Superman Returns, referring to kryptonian crystals, although their abilities are in a more realistic range.
The 1993 film Ghost From The Machine has a man build a device in his garage that can bring ghosts over from the land of the dead to the real world. Basically, a Necromancer-In-A-Box. It works on EMF-Paranormal theory, basically, ghosts like elecromagnetic activity because it lets them interact with the living.
"What do all man-made haunted objects have in common? Proxemity to power lines."
In the Expanded Universe of Daria, the Ringbearers and their weapons, the Defender Rings, fall squarely into this trope.
In Marion Zimmer Bradley's Darkover series, human colonists stranded on a metal-poor alien planet eventually develop a new "non-causative" science based on Psychic Powers and "starstones". The resulting "matrix technology" can do things believed to be impossible by the conventional technology used by other human worlds. The catch is that it only works fortelepaths, which prevents it from being built or used by anyone else.
In Anne McCaffrey's The Ship Who Won, a Role-Playing Game-obsessed space ship crew find a planet where magic seems to actually work. Then they discover there's a powerful weather control system built into the planet that can be operated through gestures and "magic words", which the inhabitants have just about broken through their overuse of it as a weapon and source of cheap magic tricks.
Council Wars series is based around this trope. Unlike most such examples, rather than being set After the End when people have long since forgotten the origin of their "magic", it's set during the breakdown of a Sufficiently Advanced society into relative barbarism.
In Orson Scott Card's Homecoming series, the deity of a human colony world, the Oversoul, is in fact an AI in orbit around the planet, which provides certain favored characters with "magical" devices to get them to return to Earth because the society it created is breaking down. Humanity is developing resistance to the Oversoul's Mormonism-inducing mind-control, leading to an outbreak of atheism and violence.
Subverted in the short story Death in Vesunna. A hot-headed time traveler shoots a Roman book dealer in order to get a book that doesn't exist in his time. The locals, who only heard the gunshot and found the corpse, assume it was "Zeus's thunderbolt", but the two men investigating the case use intelligence and logic to figure out exactly what happened.
Also subverted in The Guns of the South, the novel that made Turtledove famous. Time travelers go back to change The American Civil War in the Confederacy's favor by arming them with AK-47s. The guns are never treated as magic, simply as weapons of amazing quality whose appearance makes no sense (as a Confederate gunsmith points out, the guns simply appear out of nowhere, without any precursor models, which would still be vastly superior to anything currently available). Within a couple of years, the Confederates are producing their own copies (and the last chapter says that the United States has developed similar weapons). The same thing is true of the MREs and instant coffee the time travelers had. Dessicated foods are nothing new, just the idea of preparing coffee and whole meals that way.
Averted in the first Discworld novel, The Colour of Magic. Incompetent wizard Rincewind has sometimes wondered whether there might be something different from magic, something better. The Agatean tourist Twoflower shows up with a camera and hires Rincewind as his guide/interpreter. When Rincewind first sees it, he surmises that it could possibly work by focusing light onto paper treated with extracts from photosensitive plants, thus creating the image. Simplifying for the locals Twoflower wants to photograph, he says, "He has a demon in the box that draws pictures. Do as the madman says and he will give you gold." He's rather disappointed to discover that the box indeed contains a demon that draws pictures.
Isaac Asimov's The Last Question turns out to be Divinity From Technology.
And Isaac Asimov's first Foundation novel, the Anacreonian civilisation is basically taken over by Salvor Hardin's new religion of science. Interestingly, this wasn't the original intention of the Foundation citizens (though it was of course part of Seldon's 1,000 year plan). They simply created the religion as the most convenient way to spread atomic technology to the Four Kingdoms who have regressed into barbarism (The Galactic Spirit Did It). It's only later that they realized that they now hold power over the people of these kingdoms, if not the rulers.
HP Lovecraft's earlier Cthulhu Mythos stories were full of gods and magic. His later stories leaned more toward extraterrestrials and suggested that all magic is really super-advanced science.
He never went that far, actually. The aliens (like, say, the Mi-Go swarms) had both super-advanced technology and magical knowledge, which may have been given to them by one of the more powerful Eldritch Abomination.
In Lovecraft's world "magic" is super-advanced knowledge of the laws of the universe that humanity has only scratched the surface of. For example, in The Dreams in the Witch-House it's shown that the witches in fact use Sufficiently Advanced Mathematics to teleport immense distances and grant themselves near-immortality, but they still do it in the context of a religion, or possibly it just looks like a religion to the outsiders - the pathways beyond the three-dimensional space are guarded by Nyarlathotep, the Crawling Chaos, and he expects annual human sacrifices in return for their use - possibly simply as a sign of cutting themselves off the rest of the humanity than any practical purpose, though this isn't elaborated.
Perhaps the most plausible example of this trope appears in the Dream Park novels, Niven & Barnes' series about live-action adventure gaming at a future amusement park full of high-tech illusions. Sophisticated simulations allow fantasy combats to be played out in reality, holographic or robotic monsters battling role-players with computer-controlled magic staves and hit-point-tracking electric dog tags.
Black Trillium eventually reveals that the Big Bad is using advanced technology from a lost civilization and calling it magic.
In one story, Lord Peter Wimsey convinces the inhabitants of a small Basque village that he is a magician by using 1920s technology. ("Jesu Maria, the wizard could make music come out of a box!") It seems that this is a village so backwards and isolated that not only has not heard about the radio by the late '20s, but neither the gramophone or even music boxes.
Sharon Shinn's Samaria (Archangel) series. In the first-written novel, Archangel, the only hint we get that the angels and oracles aren't magical is a note before the story begins and the fact that the oracles use "interfaces" and apparent computer screens. In Jovah's Angel, the characters finally figure it out.
Theodore Sturgeon depicted a technology known as Logros in the novel 'Venus Plus X'. Logros was employed to do such effects as anti-gravitation, force fields, cold fusion, and many more diverse and fantastic things. But the principles behind Logros are advanced beyond any ability to describe, and all the machinery is invisible or not recognizable as technology to the uninitiated. However, we are assured that Logros is quite simple to build and use, as with any sufficiently advanced technology. For example, the underlying theory behind an electric motor is quite advanced, but the actual product is a series of simple coils of wires and magnets. Sturgeon goes on to make the statement, "Someday, we will be able to do absolutely anything with absolutely nothing, but the science behind it will be too complicated for any human or computer to comprehend."
The majority of stories where starship-era characters somehow meet medieval-era characters have the medieval-era people believe that the technology is actually magic, at least initially. Generally, it's only the trusted allies who are told that it's actually advanced technology, the bad guys are left believing it's magic, often with truly hilarious reactions. Sometimes has unfortunate consequences if there's a local Inquisition. David Weber is fond of this.
In Christopher Stasheff's Warlock of Gramarye series the main protagonist lands on a medieval world and because of his modern technology, he's taken for a magician (understandably, since magic - technically, Psychic Powers - is commonplace on the planet). It is eventually revealed that they're right.
Thieves World has Kemren the "Purple Mage" who channeled magic power from waterwheels. This setup has its own drawbacks, though.
Trapped by James Alan Gardner explains that magic on earth is actually alien nanotech that has displaced about 1/3rd of all bacteria in the entire ecosystem, including all the bacteria inside animals, and humans too. It can be controlled by people that had nanotech attach itself to the right spot in their brains while still in the womb. Where and how it attached determined the types of powers, and how they were activated. One character explained the feeling of performing magic being like having a million happy puppies eager to do his bidding.
This is the central conceit of The Steerswoman. The characters all use terminology that seems straight out of a Standard Fantasy Setting, but their world is actually much more science-fictional (the "spell"-casting "wizards" are actually people who've preserved more technology than everyone else, the "gnomes" are chimpanzees, the "demons" are Starfish Aliens, and so on).
Elizabeth Bear's Jacob's Ladder trilogy. Angels are AIs given "bodies" by means of forcefields, magic swords are products of nanotech and the "magic" of the various sorcerers, priests and necromancers are varying combinations of cyber and biotech.
Mike Resnick's The Buntline Special has Thomas Edison and Ned Buntline working under the auspices of the US government to find a way to circumvent Native American magic.
David Weber's Safehold series takes place on a planet where the original colonists were brainwashed to believe the founders were archangels, backed up of course by high tech and kept in a medieval state of technology by orbiting satellites that wipe out any example of technology that isn't muscle, wind or water powered.
In Manoratha by V. Ushakov this seems to be an unexpected side effect of the population's immersion into the eponymous MMORPG "Manoratha". The developers expected skills like martial arts or craftsmanship to carry over, since they are comparably hard and time-consuming to master. Unexpectedly, the most advanced and dedicated players begin exhibiting the first tiers of their most advanced magic schools in reality.
The Psalms of Isaak is a Science Fantasy quintet which takes place in a Scavenger WorldAfter the End. Some relics of the previous age, such as the robotic mechoservitors, are clearly understood as technology, albeit technology advanced beyond the means of most people in the setting to understand or replicate. What is usually called "magic" generally appears to be a product of advanced chemistry, since it takes the form of potions or powders which can be ingested to grant (moderately) superhuman abilities, albeit at the expense of the long-term health of repeated users. The Younger Gods had powers that are generally considered magical but when surviving Younger Gods start showing up later in the series, their powers look an awful lot like nanotechnology. On the other hand, the Younger Gods' rivals the Wizard Kings, though they draw heavily on stolen Younger God knowledge, also used Blood Magic of a blatantly mystical type that defies scientific explanation as do their spiritual descendants, The Empire of Y'Zir.
In Linda Nagata's The Bohr Maker when a superstitious slum dweller is infected with an advanced bit of nanotech (the "Maker" of the title) she interprets it as a sorcerer's curse and, when it enables her to control minds and heal people both she and her neighbors think she's become a witch.
The technicians who control the Organic Technology in the Bel Dame Apocrypha trilogy by Kameron Hurley are referred to as magicians. On the other hand there is as yet no scientific explanation for the shapeshifters.
The Star Trek: The Next Generation episode "Who Watches The Watchers" uses this explanation to convince the people that they are not gods, by pointedly asking how they themselves might be regarded by ancient ancestors who had never seen a bow and arrow strike down an animal at range.
Another episode, "Devil's Due", had a Con Artist pretending to be the planet's version of the Devil (who also claimed to be the actual Satan) who was using a cloaked ship to fake mystical powers.
Babylon 5 and Crusade had the Technomages, who used advanced technology to create the effect of magic (for example, holographic dragons). Interestingly, they're entirely forthright that they're using technology; their belief seems to be that magic is at base defined as functional artwork, artistry, or artistic intent. The trappings are an attempt to reconnect themselves and others with the inherent wonders of the universe and of manipulating these through applied will. Even more interesting is that other people actually buy into it as well. For example, after a Technomage basically infects Londo's computer with a virus, Londo himself refers to it as being "possessed by a holo-demon".
The "abilities" (i.e. superpowers) demonstrated by The 4400 are a result of the existence of an extra neurotransmitter, Promicin, in their brains due to biological modification by people from the future.
That how the existence of magic is justified in Wizards of Waverly Place—it's produced by a dragon-powered thermo-electric plant and transferred through circuit breakers in each wizarding household.
The Techno Babble descriptions of the mutations bestowing powers in Heroes is definitely in the spirit of this trope.
Many episodes of Doctor Who involve discovering this truth behind apparently supernatural menaces. (However, the truth tends to be scarier than what things looked to be at the beginning). The Doctor's race, the Time Lords, also have this going on in a BIG way. Many of their more notable pieces of technology, especially anything created by Rassilon or Omega, are magical items in all discernible respects and some are capable of potentially universal effects.
Certain of the more esoteric tech devices in Warhammer 40,000 start touching onto this trope; especially when you start seeing tech devices that interact with Psychic Powers and things having to do with the warp in general. Certain xenotech devices, like Halo Devices from Dark Heresy, definitively qualify. Despite its religious view of technology, however, most imperial tech does not come anywhere near this level.
This is actually state policy. Common folk do not understand that their machines are exactly that and refer to "machine spirits" which need to be "appeased" by "rituals" to keep them working, healthy, and benevolent. Lesser "Tech Priests" usually buy the propaganda, too. Of course, the "religious" rituals tend to be good, old-fashioned maintenance with a few hymns thrown in. Based on the author (and world), this Cargo Cult madness might be reserved for very complex machines or might result in folks sing hymns to their noble, fallen light bulbs when they burn out. Whatever the case may be, the vast, vast majority of humans truly believe technology is magic.
And yet, there are frequent reports of phenomena such as a tank continuing to fight after its entire crew has been killed. Given the level of Diabolus Ex Machina in the setting, whether this trope is truly in effect is something of a question mark.
And always it is elite tanks, created by the recovered lost technology blueprint's without the slightest understanding of it's state of the art electronic's. Not to mention the other parts. Most of the Machines Spirits are just A.I. that survived the Dark Ages. Since the Empreror prohibited all A.I., technpriest's don't even think about researching it. Well, at least that's what they keep saying.
Warhammer 40,000 Roleplay gives us the Technical Knock and Gun Blessing talents. Technical Knock allows an operator to clear a "jam" (the catch-all term used for almost all weapon malfunctions, including in flame and energy weapons) with a swift, simple ritual that may or may not be code for hitting the gun just right. On the other hand, Tech Priests can learn the Gun Blessing, which allows them to unjam multiple weapons at once with a wave of their hand.
Necrons, anyone? They have no connection to the warp, but in material world their technologies tend to surpass eldar's. They have, as of their latest Codex, a unit who can tell the laws of physics to "Piss off and quit cramping my style".
Lampshaded in d20 Past, a supplement for d20 Modern. The "Pulp Heroes" campaign setting includes a "Scientist" advanced class. One of the class features is that they make scientific discoveries, which they can then use to create technological devices by spending XP. The effects of these devices are taken from the spell lists for the "Urban Arcana" setting.
Numenera is this trope. Set a billion years in the Earth's future, the game describes that preceding civilizations before the current one (the Ninth World) have mastered intergalactic travel, nanotechnology, quantum physics, terraforming and more besides. All the wondrous locales and 'magic' of the world is performed through highly advanced technology. Wizards (or 'nano') work their spells through nanites in the air.
In the Phantasy Star games, there is both magic and magic from technology, at least in the Phantasy Star universe's history. Early on in the story however, magic ( the much more powerful of the two ), is stated to have 'died', after which it was only usable by the spiritual reincarnation of an ancient and unbelievably powerful mage. TECHNICs, however, as this became known, are initially just described as 'not magic' despite having similar, if less powerful effects to magic. In the later parts of the series (Phantasy Star Online and especially Phantasy Star Universe), TECHNICs are explained as manipulations of photonic energy by a TECHNIC user's mind, made possible by psychic amplifier technology and photon reactors built into their weapons.
The MMO Tabula Rasa is based around this - the PCs are humans with the capability to use ancient alien technology that writes information directly into their minds and lets them do seemingly magical things like shoot lightning.
The very definition of Anarchy Online. About twenty-four thousand years in the future, nanotechnology allows people to do such improbable things as throw lightning and fire, create huge, floating eyeballs that can throw lightning and fire, and survive death. How does nanotechnology allow people to survive death? No one knows: it doesn't work on any other planet.
Magic, or rather Ether, in Xenosaga is almost all derived from technology. For Ziggy, it's all functions of his cybernetic body. For KOS-MOS, an android, it's technology built into her or technology she can transport or control remotely. For the rest of the cast, it's nanomachines they control remotely to create various effects. The exception is chaos, whose magic turns out to actually be magic as we would define it.
The Wild ARMs series uses this as well. Though studied in academies like Functional Magic magic on Filgaia is actually a result of nanomachines left in the atmosphere by the precursor race who were abandoning a swiftly dying planet, not realizing that by decreasing the population like they did they saved it anyway and the world survives. Any supernatural beings or monsters arise from people or animals being altered by nanomachines. In later installments of the series magic is channeled from technological spirits called Guardians using the same principles as above.
While the entire nanomachine technology system from the Metal Gear Solid series arguably fits here, an even better example is Fortune from Metal Gear Solid 2. For most of the game, she is said to have been Born Lucky. At the end, it turns out that she has been carrying around some kind of electromagnetic device that somehow deflects bullets, stops explosions, and prevents an unstable weapon from destroying itself.
Subverted in that, after the device is destroyed, she still manages to deflect several projectiles fired at her.
Eco from Jak and Daxter works like this. Not only can it be applied to futuristic guns, but it can allow users to fire singularity blasts, slow time, conjure green crystals, erect shields, or do any number of other things.
AMP (Standing for Anti Matter Principle) technology from Final Fantasy XIII used by the Sanctum Government was modeled after natural l'cie magic and comes in handy devices called Manadrives.
Touhou PC-98 characters Rika, Rikako Asakura, Chiyuri Kitashirakawa, and Yumemi Okazaki have all used science to such degrees that spirits and fairies emerge. In the Windows series, the kappa frequently borrow and improve upon technology from outside Gensokyo, but this might be more Magitek.
In fact, the original plan for the third game was to have a big reconstructive twist where they acknowledge that, in fact, biotic abilities and the mass effect do not make sense with the conservation of energy. The energy has to come from somewhere: remember all those stars dying before their time? Whenever a ship accelerates to FTL, entropy in the universe increases massively. The Reapers, according to the original plan, were a means of delaying the heat death of the universe by destroying civilizations that have reached the point of using too much mass effect.
Most of the "Tech powers" in these games are supposed to be grenades, but in the second game, the lightning like "overload" ability hits enemies instantaneously, while the "Incinerate" ability is a fireball in all but name.
In the Guilty Gear games' backstory, a limitless energy source was eventually discovered and the scientists gave it the most appropriate name they could: magic.
NOVA in Kirby Super Star, the wish-granting comet god, is made of random mechanical parts.
In the world of the first two Might and Magic novels, magic is done by tapping into the Ancients' planetary 'Wire'. It is left unclear if this applies to the other worlds, and if the Wire is pure (if sufficiently advanced) technology or Magitek (at least some Ancient tecniques utilizes manipulation of the Elemental Planes).
The Forerunners in Halo. It is very hard to list what their technology doesn't allow them to do. To wit: hyper-advanced armor worn by everyone that renders them immortal and removes the need for sleep, solid objects made of light, truly sentient AI, mastery of gravity and FTL travel, the ability to create, destroy, and move stars and planets, create structures the size of small star systems, and so much more.
The page quote is said word for word after a certain technology is discovered in the Civilization V scenario "Empire of the Smoky Skies".
In Shin Megami Tensei, the demonic realm can be breached though certain forms of teleportation, and computers can be used to summon, store and handle demons (albeit through the use of a Black Box-laden program).
In the Inherit The Earth: Quest for the Orb the titular Orb of Storms was created by sufficiently advanced humans. It has been used for generations to judge the growing and planting seasons and its holders have a huge advantage in managing their food supply. It's apparently the core operating system for some weather control satellites.
The encyclopedic analyzing ability of the voice-activated Orb of Hands is also used to help with construction and the creation of tools.
The vast majority of technology seen in Heliothaumic is derived from centuries of study of the titular Heliothaumic energy that is derived from the sun, either using solar panels or thaumite.
In Gunnerkrigg Court, a binding spell used to negate the powers of a Body Snatcher turns out to be a kind of computer program. However, the computer itself contains magic parts. Magic itself is referred to as the "etheric sciences", sometimes (Kat is confounded to discover that her parents believe in magic, and more so to find out that it's a known quantity not dissimilar to her beloved robots and computers).
Seems to be the case in Homestuck, or at the very least Eridan seems to believe so, with his White Magic of SCIENCE as he calls it. Doc Scratch agrees with him. However there are still inexplicable superpowers, gods, and even the technology has baffling origins. Eridan's own White Magic is implied to have been a corruption of his own superpowers, making his SCIENCE incorrect.
In The Monster And The Girl, Kenrick has a 'BIST' which seems to be like technological version of a D&D 'Bag of Holding', and Kenrick is described as a 'techno-magical' Cyborg created by a mad alien god. The implication is that it's all super-science.
The Powerpuff Girls were made from Sugar, Spice and Everything Nice. And a bottle of Chemical X.
Used and averted in Young Justice, where Kid Flash attempts a technobabble explanation to Doctor Fate's genuine mystical powers. Klarion the witch boy, another magic user, observes this and mocks his current minion Abra Kadabra with the fact that Flash has identified the precise method that he uses to pretend to have magical powers.
The Dora the Explorer episode "Boots' Banana Wish" has a wishing machine, which can grant any wish. Though it is prone to breaking from too many double negatives.
Practioners of Chaos Magic and Technoshamanism believe that this is essentially true.
Think for a moment (in the most generalized way) about what your computer really is. It is an absurdly complex machine that does nothing but add ones and zeroes together really fast. Despite this, layer upon layer of abstractions built on top of this most basic of arithmetic allows you to not only write with light but create images, store sound and produce seemingly intelligent, interactive responses using nanometer-scale metal circuits and plain old electricity. 50 to 80 years ago this would be considered such abuseofbasic science that only the softest of Sci-Fi writers—or those writing outright Science Fantasy—would have dared to touch it. For some, thinking about it too deeply can destroy your Willing Suspension of Disbelief in real life. Adding the global Internet into the picture just adds another layer of Mind Screw to the whole thing.
There have been a few cases where human beings with less advanced technology encountered objects from societies with more advanced technology and came to the conclusion, "Magic." In some cases, the less technological society has converted religions since clearly the other society's god(s) were more capable of giving their "shamans" power. Cargo cults are one such case. These members generally believe benevolent spirits/ancestors/gods made the manufactured goods and sent them to the more technological society whether due to the rituals and temples (shipping manifests, radio calls, piers, airstrips, etc) of the other group or because these rituals tricked the benevolent spirits to sending the goods. The cult mirrors the actions taken by their more technologically endowed neighbors in order to get the goods themselves. The locals had no experience of modern industry and tended not to believe the explanations given to them.
Likewise this happens with missionaries. If a group had no modern theory of disease and sees many children die to a disease, they'll likely conclude evil spirits or something supernatural is responsible. If missionaries, who generally mean well whether you agree with them or not, hand out little tablets that make the disease go away, the locals most likely conclusion is, "Jesus's magic is way stronger than whatever we've been doing before." The other common scenario was missionaries bringing lethal European diseases with them, leading the locals to believe that the missionary's magic was to blame for their illness.
We now have access to a lot of "magic devices" from fairy tales:
A magic mirror that can show who is the fairest in the land. (Google image search)
A magic mirror that allows instant communication all over the world. (Cell Phones)
A mop that cleans the house by itself. (Roomba vacuum cleaners.)
A carriage that drives itself. (Computer-controlled cars, albeit still in the experimental stage.)
Magic fire. It can be lit and extinguished at will, and able to burn brighter than any ordinary fire (light bulbs). Even old technology can seem like magic to those who came before.
A History Channel documentary about scientific prophecies of doom included men discussing the impending disasters such as total economic collapse and other such global tragedies. One commented that the current age of man is entirely dependent on oil products that are little more than magic in what they have allowed us to achieve; take away the oil, however, and...
Though most are still in the early prototype stage, a number of devices like Epoc's Emotiv controller use EEG technology to read your brainwaves and transmit commands wirelessly to a nearby computer. Depending on how that computer is programmed—and what hardware is attached to it—you can effect changes on the world around you ranging from changing the color of an object on-screen to driving a car, just by thinking about it.
Eventually? Sony has been working on feeding sensory information directly to the brain for over a decade, at least. In 2006, they reported that they had successfully caused a subject to see the color blue, and were able to consistently replicate it. It's just a matter of time before we get full-immersion virtual reality.
Magicians often accomplish their feats this way. While a lot of magic is done with sleight of hand and knowledge of human perception and psychology, many magicians create entirely new devices to make their tricks work.
Magic Shell, the ice cream topping that pours out of a bottle but becomes hard enough to break with a spoon after a few minutes may look like magic until you know it relies on coconut oil. Said oil turns solid when exposed to the temperatures ice cream comes out of the freezer at and melts at around room temperature. (This is why you should warm up the bottle if the magic refuses to flow.)