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*Any Japanese cards below may be poorly translated*
Yu-Gi-Oh the Movie (1)
The movie opens in a manner similar to Season 1 with a story of how Yugi's story came together but with a few changes. We find Yugi struggling to solve the Millennium Puzzle as a homage to Season 0 while a dark entity moves around. Elsewhere, archeologists are digging and find the lost tomb of Anubis. As Yugi finally gets down to the final piece, the archeologists discover a door that opens to an object like the Millennium Puzzle. The puzzle is completed and the archeologists become trapped until the door is destroyed. Worse still, the other archeologists outside cannot escape before being dragged down. Back in the Game Shop, Duel Monster spirits emerge from the Millennium Puzzle and Yugi finds himself surrounded.
Unable to fight them, Yugi becomes Atem and Atem is successful at getting rid of them. However, since the Millennium Puzzle has been solved, the Shadow Games will begin again. Meanwhile, everyone watches the news telling of Yugi's success (and using Japanese footage because the Exodia the Forbidden One card isn't formatted like the dub cards). What is known is that Yugi has proven himself in Duelist Kingdom and Battle City where he defeated Seto Kaiba for the championship (which is incorrect, though they do show the scene where Atem gets Ra from Marik). Some duelists aren't so convinced and feel confident they could beat him with ease. Players get their Duel Disks ready but can any of them defeat Atem or the God Cards?
(Well a few did succeed but Atem didn't have the God Cards during any of those times). We find Atem and Kaiba in the midst of a duel (and Japanese LP graphics are being used in spite that this was first released in English). Kaiba is determined to beat the God Cards and uses Polymerization (which has the TCG design for the first time as do the rest of the cards but I'm only noting it here and strangely, it has the original errata of the card as the later prints have longer text, not to mention that it's a Spell Card, when that lore was only associated from when it was a Magic Card) to bring out Blue-Eyes Ultimate Dragon (4500) in Attack Mode. After that, he doubles BEUD's ATK with Megamorph, raising its ATK to 9000.
However, Atem is ready and uses Obelisk's effect to tribute Ra and Slifer to make Obelisk's ATK infinite. Nevertheless, Kaiba attacks and loses but we find it's a simulation. Kaiba's men were certain they had the perfect strategy and want another chance but Kaiba refuses and fires them. Kaiba knows there must be a way to beat the God Cards and knows where to start looking. We find Pegasus asleep in his bedroom while a spirit inserts a card into his Deck. Pegasus finds himself in a dream where the God Cards are sealed away and makes a vow not to have white wine spritsers before bed. Even though he doesn't have his Millennium Eye anymore, Pegasus feels something terrible is about to unfold.
Back in the game shop, Solomon is reading the paper when the new pendant catches his eye and decides he must see it for himself. Meanwhile, Kaiba takes off as the song "You're Not Me" plays before Kaiba lands at Pegasus' estate just as Pegasus gets a red whine spritser from Croquet. Kaiba is in no mood for Pegasus' games and explains his situation but Pegasus doesn't feel Kaiba is worthy of such a card and confesses to having one. Not willing to back down, Kaiba agrees to wager his Blue-Eyes White Dragons in a duel for the card. Pegasus agrees and while they get set up, Yugi and the gang discover the crowd of duelists itching to duel Yugi for the God Cards but Tea` steps in to take Yugi away while Joey and Tristan fend them off.
As Joey and Tristan start to leave, they're convinced to stay and Joey agrees to duel with his opponent being the one that started it all. The other duelist draws and summons Injection Fairy Lily (400) in Attack Mode (and at 18:04 into the movie, the card is completely mirrored as you can see the card's properties on the opposite side they should be). He attacks directly (though it's unclear whether he's powered up IJL or not but probably so yet this duel doesn't follow official rules because Joey's opponent wouldn't be allowed to attack on the first turn). Later, Joey gets involved with another duel where the 2nd opponent tributes Fenrir and Inpachi for Great Maju Garzett (0000) in Attack Mode (and its ATK becomes the combined ATK of the tributed monsters, making its ATK 3000. He takes out Gearfried with it (but it's unclear what his score was beforehand). Joey draws and tributes his remaining 3 monsters for Gilford the Lightning (2800) in Attack Mode and destroys GMG.
Yugi appears asking about the coast being clear but he and Tea` quickly see that it isn't and she drags Yugi away while the crowd of duelists give chase and run over Joey and Tristan. Yugi and Tea` hide behind a wall and while she figures out a place to hide, Pegasus and Kaiba get set up for their duel. Pegasus draws and activates Toon World by paying 1000 LPs, bringing his score down to 3000 and gets ridiculed for it. Next he summons Toon Gemini Elf (1900) in Attack Mode (and this card doesn't have the proper fonts or text on its card as shown at 20:48 into the movie). With that, Pegasus sets 1 card to end his turn so Kaiba draws and summons X-Head Cannon (1800) in Attack Mode before setting 2 cards to end his turn.
Pegasus plays being scared, then draws and uses Card of Sanctity to force both players to draw cards until they each have six cards in their hands. (The real card forces you to remove from play all cards you control and in your hand to draw until you have 2 cards in your hand.) Next he uses Cost Down to discard 1 card and make his monsters' Levels drop by 2. Then he summons Toon Dark Magician Girl (2000) in Attack Mode (which was shown as Dark Magician Girl in his hand earlier). He attacks Kaiba directly, bringing Kaiba down to 2100 LPs and forcing Kaiba to randomly lose Monster Reborn from his hand.
His direct attack with Toon DMG forces Kaiba to activate Attack Guidance Armor to make TGE the attack target, destroying it instead and leaving Pegasus down to 2900 LPs. Pegasus isn't worried as he uses Monster Reborn to revive Toon Gemini Elf. Next he activates Ultimate Offering, letting him pay 500 LPs to Normal Summon again (which based on his Deck is completely unnecessary in the CG as the Toons cannot be Normal Summoned or Set apart from a few). He does so, bringing his score down to 2400 and summons Blue-Eyes Toon Dragon (3000) in Attack Mode by Tributing TGE. Next he pays again and summons Toon Summoned Skull (2500) in Attack Mode, bringing his score down to 1900.
Yu-Gi-Oh the Movie (1)'s Episode Cards

Card Info:

Polymerization (original artwork)
Normal Spell
Fusion Summon 1 Fusion Monster from your Extra Deck, using monsters from your hand or your side of the field as Fusion Materials.
Found In: Structure Deck: HERO Strike
Set #: SDHS-EN023
Rarity(s): Common
Notes: Yu-Gi-Oh the Movie: It fused monsters.
Card User: Seto Kaiba

Card Info:

Blue-Eyes Ultimate Dragon (original artwork)
LIGHT / Dragon-Type Fusion / Level 12 / ATK 4500 / DEF 3800
"Blue-Eyes White Dragon" + "Blue-Eyes White Dragon" + "Blue-Eyes White Dragon" 
Found In: Japanese Duelist Road: Piece of Memory Yami's Side and Yugi's Side
Set #: 15AX-JP000
Rarity(s): Ghost Rare
Notes: None
Card User: Seto Kaiba

Card Info:

Megamorph
Equip Spell
While your Life Points are lower than your opponent's, the equipped monster's ATK becomes double its original ATK. While your Life Points are higher, the equipped monster's ATK becomes half its original ATK.
Found In: Structure Deck: Cyber Dragon Revolution
Set #: SDCR-EN024
Rarity(s): Common
Notes: None
Card User: Seto Kaiba

Card Info:

Injection Fairy Lily
EARTH / Spellcaster / Level 3 / ATK 400 / DEF 1500
If this card attacks or is attacked, during damage calculation (in either player's turn): You can pay 2000 LP once per battle; this card gains 3000 ATK during that damage calculation only.
Found In: Super Starter: Power Up Pack (YS14)
Set #: YS14-ENA07
Rarity(s): Super Rare
Notes: Duelist's name wasn't given so I gave him one.
Card User: Patrick

Card Info:

Great Maju Garzett
DARK / Fiend / Level 6 / ATK 0 / DEF 0
The ATK of this card becomes twice the original ATK of 1 monster that you Tributed for the Tribute Summon of this card.
Found In: Dark Crisis (Unlimited Edition)
Set #: DCR-EN063
Rarity(s): Common
Notes: Duelist's name wasn't given so I gave him one.
Card User: Carl

Card Info:

Gilford the Lightning (2nd artwork)
LIGHT / Warrior / Level 8 / ATK 2800 / DEF 1400
You may sacrifice 3 monsters you have in play to Summon this card. When you do, you can destroy all monsters your opponent has in play.
Found In: Japanese Duelist Road: Piece of Memory Yugi's Side
Set #: 15AX-JPM17
Rarity(s): Secret Rare and Millennium Rare
Notes: None
Card User: Joey Wheeler

Card Info:

Toon World (original artwork)
Continuous Spell
Pay 1000 Life Points to activate this card.
Found In: Legendary Collection 3: Yugi's World Mega Pack
Set #: LCYW-EN115
Rarity(s): Rare
Notes: None
Card User: Maximillion Pegasus

Card Info:

Toon Gemini Elf
EARTH / Spellcaster-Type Toon / Level 4 / ATK 1900 / DEF 900
This card cannot attack the turn it is Summoned. If "Toon World" on the field is destroyed, destroy this card. While you control "Toon World" and your opponent controls no Toon monsters, this card can attack your opponent directly. If this card inflicts battle damage to your opponent: Discard 1 random card from your opponent's hand.
Found In: Battle Pack 3: Monster League
Set #: BP03-EN014
Rarity(s): Rare and Shatterfoil Rare
Notes: None
Card User: Maximillion Pegasus

Card Info:

X-Head Cannon
LIGHT / Machine / Level 4 / ATK 1800 / DEF 1500
A monster with a mighty cannon barrel, it is able to integrate its attacks. It attacks in many ways by combining and separating with other monsters.
Found In: Starter Deck: Kaiba Reloaded
Set #: YSKR-EN007
Rarity(s): Common
Notes: None
Card User: Seto Kaiba

Card Info:

Card of Sanctity
Japanese Normal Spell
Remove all cards you have in play and in your hand from play. Draw cards until you have 2 cards in your hand.
Found In: Japanese Duelist Road: Piece of Memory Yami's Side
Set #: 15AY-JPC27
Rarity(s): Ultra Rare
Notes: Yu-Gi-Oh the Movie: It forced both players to draw cards until they had six cards in their hands.
Card User: Maximillion Pegasus

Card Info:

Cost Down
Normal Spell
Discard 1 card; until the End Phase, reduce the Levels of all monsters in your hand by 2 (even after they are Summoned).
Found In: Duelist Pack: Kaiba (Unlimited Edition)
Set #: DPKB-EN033
Rarity(s): Rare
Notes: None
Card User: Maximillion Pegasus

Card Info:

Toon Dark Magician Girl
DARK / Spellcaster-Type Toon / Level 6 / ATK 2000 / DEF 1700
Cannot be Normal Summoned/Set. Cannot be Special Summoned unless you control a face-up "Toon World". Must first be Special Summoned (from your hand) by Tributing the same number of monsters needed for a Tribute Summon (normally 1). If "Toon World" on the field is destroyed, destroy this card. This card can attack your opponent directly, unless they control a Toon Monster. If they do control one, this card must target a Toon Monster for its attacks. This card gains 300 ATK for every "Dark Magician" or "Magician of Black Chaos" in either player's Graveyard.   
Found In: Legendary Collection 3: Yugi's World Mega Pack
Set #: LCYW-EN111
Rarity(s): Rare
Notes: Yu-Gi-Oh the Movie: It was Normal Summoned.
Card User: Maximillion Pegasus

Card Info:

Attack Guidance Armor
Anime Normal Trap
Activate only when an opponent's monster declares an attack. Make an opponent's monster the attack target, then calculate damage.
Found In: Not Yet Released
Set #: None
Rarity(s): Common
Notes: None
Card User: Seto Kaiba

Card Info:

Monster Reborn
Japanese Normal Spell
Choose a monster in either player's Graveyard and Special Summon it to your field.
Found In: Japanese Duelist Road: Piece of Memory Yugi's Side
Set #: 15AX-JPM38
Rarity(s): Secret Rare and Millennium Rare
Notes: Yu-Gi-Oh the Movie: Its artwork was different.
Card User: Maximillion Pegasus

Card Info:

Toon Gemini Elf
EARTH / Spellcaster-Type Toon / Level 4 / ATK 1900 / DEF 900
This card cannot attack the turn it is Summoned. If "Toon World" on the field is destroyed, destroy this card. While you control "Toon World" and your opponent controls no Toon monsters, this card can attack your opponent directly. If this card inflicts battle damage to your opponent: Discard 1 random card from your opponent's hand.
Found In: Battle Pack 3: Monster League
Set #: BP03-EN014
Rarity(s): Rare and Shatterfoil Rare
Notes: Special Summoned by Monster Reborn's effect.
Card User: Maximillion Pegasus

Card Info:

Ultimate Offering
Japanese Continuous Trap
You can pay 500 Life Points to play a monster from your hand as a Normal Summon or Set during your Main Phase or your opponent's Battle Phase.
Found In: Japanese Duelist Set Version Machine-Gear Troopers
Set #: DS14-JPM38
Rarity(s): Ultra Rare
Notes: Yu-Gi-Oh the Movie: Its artwork was different.
Card User: Maximillion Pegasus

Card Info:

Blue-Eyes Toon Dragon
LIGHT / Dragon-Type Toon / Level 8 / ATK 3000 / DEF 2500
Cannot be Normal Summoned/Set. Cannot be Special Summoned unless you control a face-up "Toon World". Must first be Special Summoned (from your hand) by Tributing the same number of monsters needed for a Tribute Summon (normally 2). This card cannot attack the turn it is Special Summoned. You must pay 500 Life Points to declare an attack with this monster. If "Toon World" on the field is destroyed, destroy this card. This card can attack your opponent directly, unless they control a Toon Monster. If they do control one, this card must target a Toon Monster for its attacks.  
Found In: Legendary Collection 3: Yugi's World Mega Pack
Set #: LCYW-EN103
Rarity(s): Rare
Notes: Yu-Gi-Oh the Movie: It was Normal Summoned.
Card User: Maximillion Pegasus

Card Info:

Toon Summoned Skull
DARK / Fiend-Type Toon / Level 6 / ATK 2500 / DEF 1200
(This card is always treated as an "Archfiend" card.)
Cannot be Normal Summoned/Set. Cannot be Special Summoned unless you control "Toon World". Must first be Special Summoned (from your hand) by Tributing the same number of monsters needed for a Tribute Summon (normally 1). This card cannot attack the turn it is Special Summoned. You must pay 500 Life Points to declare an attack with this monster. If "Toon World" on the field is destroyed, destroy this card. This card can attack your opponent directly, unless they control a Toon Monster. If they do control one, this card must target a Toon Monster for its attacks.
Found In: Legendary Collection 4: Joey's World Mega Pack
Set #: LCJW-EN237
Rarity(s): Rare
Notes: Yu-Gi-Oh the Movie: It was Normal Summoned.
Card User: Maximillion Pegasus