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- Throughout the franchise, any time there's some ancient text on-screen, often it is actual text. Hieroglyphics are used accurately, and the lettering on the Seal of Orichalcos is Enochian, and spells out the card's name (once on each side of the seal). This extends to Orichalcos Deuteros and Orichalcos Tritos, too.
- The Anatomy of the Soul is faithful to Ancient Egyptian belief. The ka was the force that gave you life, essentially your spirit or life force, while the ba was everything unique about you, basically being your mind and personality. Upon death, each day the ka goes to the afterlife (essentially to live it up in paradise) and the ba stays in the physical world to watch over your family, and they return to the physical body in the evening to rest. The franchise adapts this with ka being the monster spirit one can summon, and ba being their life force they must use to manifest that spirit.
- As an extension of this, names were very important in Ancient Egypt because it was believed that if a person's name was not inscribed in their tomb, the ka and ba would get lost trying to return to the body and you would be truly gone, your spirit unable to go to the afterlife or watch over your family. This is why Pharaoh Atem's name is so important and retrieving it symbolically allows him to leave Yugi and go to his eternal rest.
- Noah's deck references the creation of the earth from Genesis, adapted to the evolutionary development of the world. He starts with a primordeal wasteland populated by demi-human monstrosities, then a great flood wipes it all out to clear the way for the dinosaurs, until an asteroid impact kills them and allows humans to evolve to dominant life. Discounting his first two turns when he's staying in the primordeal Earth phase, Noah takes seven turns in the duel, his seventh turn being when he summons Shinato as symbolic of God and "wins" the duel. His second deck being a Spirit deck symbolizes the transition to the afterlife and spiritual plane.
- The word "Orichalcos" is a reference to Orichalcum, the metal mentioned in the original Atlantis story from Plato that was the source of Atlantis' wealth and power. It's unknown which metal Orichalcum actually was, but is generally believed to be some sort of copper alloy, which would fit with the green color of the Orichalcos.
- The Knights of Atlantis are named for the three characters other than Platos and Socrates that appear in Plato's dialogues describing Atlantis, with Hermos being shortened from Hermocrates.Red: Yu-Gi-Oh! knew more about Atlantis then I did... that one... that one kinda stung.
- In The Dark Side of Dimensions, Aigami's Cubic deck references Buddhism and the "Guardians of the directions", deities who rule the ten dimensions of space.
- Amnael's Alchemy deck contains six "Alchemy Beast" monsters and Golden Homunculus, reflecting the seven base metals that ancient world alchemists recognized. Meanwhile his Spell cards reference the four stages of the alchemical process, which each had their own name and associated color that are accurately represented by Amnael's cards. When he transitions to his Helios series (which have three forms of escalating power), it's a reference to Hermes Trismegistus, "thrice-greatest Hermes", the man who created the foundations of Hermeticism. Hermeticism teaches there are three parts to how the universe operates — Alchemy, Astrology, and Theurgy (the study of how the Gods work and a type of magic that is counterpart to Goetia, the study of Demons). This symbolizes that Amnael has mastered Alchemy and Astrology, but the Sacred Beasts/Phantom Demons lay beyond his grasp.
- The monster that defeats him is Electrum/Elixier, also a reference to alchemy, being the fusion of all four basic elementals to form the ultimate E-Hero, and named after both of alchemy's end goals: the creation of precious metals (electrum being an alloy of gold and silver), and the creation of the elixir of eternal life.
- In fact the series has an amazing amount of references to alchemical symbolism. For example, the motif of three suns that is a recurring element throughout the series: Amnael's ace monster, the triple suns two of the alternate worlds possess, and Nightshroud's black sun is a reference to one of the three.
- Each arc also represents a part of the alchemical process (though not necessarily in the correct order):
- Nigredo, the black, putrefying stage: Nightshroud's plot to break down humanity into a homogenous base form within his world of darkness.
- Albedo, the white, purifying stage: The Light of Destruction's desire to "purify" the world into white nothingness.
- Citrinitas, the yellow, awakening stage: Yubel's awakening of Judai's past and powers (giving him yellow eyes as the Supreme King).
- Rubedo, the red, completion stage: The fight over the sacred beasts and their ability to offer eternal youth, one of the end goals of alchemy. Also Judai being in the red dorm, representing his role as the ultimate alchemist.
- Saiou's Tarot themed Arcana Force deck often has symbolism in his cards that reflects either what is happening in the duel or something about his opponent. For instance, against Manjoume, he uses Suit of Sword X and it stops upright; this represents defeat and the anguish and despair that accompanies loss, but there is also a glimmer of hope for things to improve, like how Jun has repeatedly lost to Judai and is doubting his skills, but he can find new purpose if he joins the Society of Light. When Saiou claims his cards give him insight on his opponent, he's completely serious.
- Kabukid (Orlando in the dub) plays a Kabuki deck with many references to the story of Benkei, a popular figure for Kabuki performances.
- Eisenstein's deck contains many references to science, particularly the famous "Schrödinger's Cat" thought experiment.
- The Earthbound Immortals' names are the Quechuan words for the animal they represent; the Quechua people are a diverse South American group that, of course, included the Inca civilization that build the Nazca Lines.
- Rex's Inca deck is full of monsters symbolizing and/or based on Incan deities; for instance, Inti is the Incan sun god and Quilla is the moon goddess. When the archetype got new support in the real life card game, Envoy Oracle of Ascator and Reaper Oracle of Supay were revealed on the Japanese Twitter account at 6 am and 6 pm, Japan standard time, fitting for representing the sun and moon.
- In Bonds Beyond Time, when Malefic Paradox Dragon is destroyed, Paradox activates Malefic Paradigm Shift to summon Malefic Truth Dragon. This emulates the progression of philosophical and scientific knowledge: a contradiction (paradox) forces the thinker to reconsider the whole system and propose another general explanation (Paradigm Shift) to achieve true knowledge (represented by Truth).
- The names of the members of Yliaster — Paradox, Antinomy, and Aporia — are named after logical fallacies and impossibilities in Greek philosophy. Fitting given the Yliaster is trying to cause a Temporal Paradox. Each name fits their role too.
- Paradox: A self contradicting premise. Paradox tries to use duel monsters to prevent the same game from ever taking root in the past.
- Aporia: The confusion resulting from different pieces of evidence supporting different conclusions. Each of Aporia's three components are a different take on the same person.
- Antinomy: Two or more premises that are incompatible despite both being logically true. Antinomy is both the friendly Bruno and the antagonistic Dark Glass.
- Z-one's Timelords are based on the elements of the Sefirot. Z-one also summons each Timelord in its order on the Sefirot, and when he has multiple ones on the field, attacks in that order too.
- Episode 19~20 has Kyuando using a quiz gimmick, where the action cards require you to answer correctly to get a positive result. One of the questions was to prove Fermat's Last Theorem, which wasn't proven until almost four hundred years after it was first proposed.
- Emma's Altergeists are based on female spirits and ghosts, with their names combined with computer terminology.
- The Tower of Hanoi's design is based on the mathematical puzzle Tower of Hanoi. with 6 rings composing the levels.◊
- As Dr. Kogami states in the show, he named the Ignis after the Theft Of Fire mythological story.
- Lightning's quotes to Blood Shepherd before their fight is taken from the The Divine Comedy:"Through me you pass into the sparkle of woe.""Through me you pass into anguishing brilliance.""Through me among the light lost for aye.""All hope abandon ye who enter here."
- Yusaku's deck monsters are based on actual computer terms which his fitting for him as a hacker. Each of his aces follow a certain theme:
- Firewall Dragon is obviously named after firewalls, Security Dragon is a reference to computer security, Proxy Dragon is named after proxy servers and Honeybot is based on a honeypot, a computer security mechanism.
- Firewall Dragon's attack name is actually a cyber attack of a technology which work on the principle of intercepting electromagnetic radiation emissions from electronic devices such as monitors, hard disk and PC memory from a remote location, and allow the replay of the information captured. The technology name is called a Telecommunications Electronics Materials Protected from Emanating Spurious Transmissions or "TEMPEST" for short. So the attack on it is called a "Tempest Attack".
- The Code Talker Monsters reference some applications and terms, like Excode talker for Xcode and Transcode talker for Transcoding.
- Cyberse Clock Dragon and its summon materials are named after clock rates which is the frequency at which the clock generator of a processor can generate pulses and is used as an indicator of the processor's speed.
- Cyberse Quantum Dragon's name is a reference to quantum computing, a form of computing that utilizes quantum-mechanical phenomena, such as superposition and entanglement.
- Firewall Dragon Darkfluid card is named after Dark Fluid, an alternative theory to both dark matter and dark energy in which it attempts to explain both phenomena in a single framework.
- Revolver's Topologic dragons got their name after topology, which is the study of the properties of space that are preserved under continuous deformations. This is referenced by their designs having Mobius strip formations in all their wings and tails.
- Until Uranus broke the trend when it was released many years later, the Agent series was based on the seven planets of antiquity and the Greek gods they shared names with, with Master Hyperion representing the Sun.
- Artifacts are based on pseudo-mythological weapons.
- The Bujin series is chock full of references to Japanese Shinto mythology, such as their "boss" monsters being based on the triad of Amaterasu, Tsukuyomi, and Susanoo, along with Kagu-tsuchi and Awashima.
- The Burning Abyss series are all themed after demons from Dante's Inferno.
- The Chronomaly series is based on mysterious historical artifacts, like the moai, the crystal skulls, the Nebra sky disc, and more. Their Xyz cards, with the exception of Chrononaut, are based on historical and mythological archeological sites, like Machu Pichu and Atlantis.
- The Entity series are explicitly based on the Cthulhu mythos and the works of H.P. Lovecraft. The series does not contain the actual Cthulhu though, preferring to reference some more obscure Lovecraftian creatures like Cthugha and Hastur.
- The Gladiator Beasts are named after famous Roman warriors and conquerors.
- All Karakuris are required to attack if able and automatically switched to defense mode when attacked. Real-life karakuri were 17th to 19th century Japanese automatons that could only move in a predetermined pattern until interrupted or switched off.
- Within the Noble Knights and their Noble Arms cards, they're not only named for characters and concepts from Arthurian lore, but their card art contains hidden references to the legends. For instance, Ignoble Knight of High Laundsallyn is wielding the Arfeudutyr and Excaliburn swords and has a shadow of the Lady of the Lake behind him. Laundsallyn is based on Lancelot, who wielded Arfeudutyr's namesake sword Arondight, and was raised by the Lady of the Lake who gave Arthur Excalibur. The series also identifies Caliburn as the sword in the stone and Excalibur as the sword given by the Lady of the Lake, when most modern Arthurian adaptations merge the two weapons and depict Excalibur as the sword in the stone.
- The Railway series are designed after real-life locomotives.
- The card "True King of All Calamities", specifically its Japanese name. A Level 9 Xyz monster, it can be summoned using the three "True King" cards: "True King Agnimazud, the Vanisher", "True King Bathrastos, the Fathomer", and "True King Lithosagym, the Disaster". Its Japanese name references the combination of those three titles, "V.F.D.". This is also an abbreviation of "Vicarius Filii Dei", or "Representative of the Son of God", a title said to have been given to Saint Peter, the canonical first Pope. However, this title was also read by opponents as proof that the Pope was a representative of Satan... in the Japanese name, the "V.F.D." is read as "The Beast", which adds another Genius Bonus as the title above can also be calculated to sum to 666.