"There's a bond between my brother and me. Even when the world crashes down on you, you continue fighting."
—May, providing the Title Drop for the story.Between My Brother and Me is a crossover fanfiction written by Green Phantom Queen. It takes place at the end of the Battle Frontier arc of Pokémon, and put in the beginning of the Waking of Dragons arc in Yu-Gi-Oh! May decides to head off to home before going to Johto. On the cruise home, she gets a nightmare of Manaphy and Samiya being destroyed by a shadowy creature. When she and Max arrive home, their parents suggest that they take a vacation to the safe Domino City. At night, May is awakened by voices to head off to the basement and soon awakens a spirit calling himself Atem who states that Yami is actually one half of his soul split into two who warns her about a great evil.Joining by her side is her band of Pokémon and her little brother Max as they head off to Domino City, uncover their destinies, get some dueling done, and save the world. In the span of one week, their lives change forever.So begins the story's first three chapters. Even with a common crossover idea, Green Phantom Queen blends what she knows about the Pokémon world with the Duel Monsters of Yu-Gi-Oh! to create a dark crossover. There are also many common themes that are crossed in the story ranging from doing evil for good, doing good but not good and revenge before reason to letting bygones be bygones, standing up for your rights and fighting opposing fate. This crossover is a Deconstruction on the crossover genre and how the story line would change to benefit them for better or worse.However, this story is somewhat dark once you get past the halfway mark. Do not expect the rules of the Pokémon universe to apply to Yu-Gi-Oh! villains that want to steal souls to empower an ancient deity. It soon becomes important for the characters to grow up and face their problems dead on, or else let the world become destroyed.It is currently on hold at 28 chapters, but it is worth a read. You can read it here 
This fanfic provides examples of:
Absurdly Sharp Blade: Raphael's knife is seen cutting through May's arm to the point where it's caked in blood. He then trades it in for a sword that can seal souls.
Achey Scars: Poor, poor May... Even the best medicine in the world can't stop the bad guys from grabbing onto her bandaged wrists.
Action Girl: May shows her stuff in 'Wrath of a Goddess'. In order she, sics her Pokemon at the Swordsmen, defeats Mai in an Orichalcos Duel, goes into an amazing ploy to escape the Swordsmen and stands her ground when she gives a speech to the Swordsmen...unfortunately the last one causes her to fall to her death.
Adult Fear: Letting your kids head off to a town for a week is okay. Finding out that your daughter got her arms sliced in half and fell from an exploding building and has a man stalking her is NOT okay.
You know what makes it worse? She might not have been the only one that would get it...
After Action, Villain Analysis: May dabbles with it, but mostly before she lays the beating on her opponent. Shadow, on the other hand, has no problem explaining the darkness in the hearts of her victims, but also loves to rub it in their faces.
All There in the Manual: In-universe: May and Max learn all they need to know about dueling from a magazine called 'Duelist Monthly'...that their mom had for some reason. From it, they learned about Duelist Kingdom, Battle City and the 'who's who' in the world of dueling.
Always Need What You Gave Up: What's the best way to make sure the Great Leviathan doesn't become strong? switch a very powerful card with a fake and carry the real card on you! Yeah...it ends into disaster.
Always Save the Girl: Subverted. May, being the one captured, saves herself from having her soul taken. Unfortunately, no one could save her from getting attacked by the Swordsmen of the Orichalcos, nor could they save her from becoming corrupted by the Orichalcos.
Amulet of Dependency: May's deck carries a special card called 'Revenge of the Dark King' which boosts the attack strength of all her Dark Monsters. While it is prominent in almost every duel in the story, it's used against her when Arkana duels her and activates the card.
Anyone Can Die: In Ancient Egypt, you can. Hara and Moka—who would eventually become reincarnated as May and Mokuba respectively—got killed by the SAME person, not knowing what was going on.
Armor-Piercing Question: Subverted. May asks a question to the Swordsmen as to why they keep following Dartz's words. Unfortunately, the Orichalcos takes control before May finishes her speech so they never hear the question.
May: "Then what's your (Raphael, Valon and Alister) decision? Let's just say Dartz gets the Pharaoh's soul AND The Winged Dragon of Ra, and summons Leviathan. Let's say that the world does become paradise and that there is peace in the world. What is it going to change? Raphael's family still forgets about him, Alister's brother won't return anytime soon, and Valon is branded as a criminal! All of you guys need to wake up! Dartz is using you for his own schemes! He doesn't care about you at all; all he sees are potential souls that are going to be fed to the Great Leviathan!"
And we also cannot forget Mokuba's speech. He's speaking this to a man who's monster will obliterate him and take his lifepoints away. He's going out with a bang and smiling at it.
Mokuba: (to Alister) Master Dartz chose you, but do you choose?! Do you really want to use violence to end violence? You are who you choose to be Alister; you don't have to be someone who uses missiles and bombs to bring out your vengeance.
Armor-Piercing Slap: After Raphael states his perverted oath to bring May back to him, she does this. This is AFTER the hell of Wrath of a Goddess and it's capped off with her vow to stop him.
Artifact of Doom: The Orichalcos shard is May's artifact, as it created her darker half, Shadow.
Author Appeal: The author loves Dark monsters, giving May a deck completely filled with them. May's darker half Shadow also uses monsters with the Dark Attribute
Badass Adorable: Jirachi and Manaphy brought their attacks into Duel Monster form. It rocks.
Jirachi has Doom Desire, strong enough to cause a geyser of light to erupt and help Max win his first duel against Arkana. He's also cute whenever he's hugged by Max.
Manaphy's Heart Swap also has become badass. It doesn't make people change bodies, it makes duelists swap duel monsters and transforms the monsters into Water type, AND it also gains an attack boost from that. Also, its Hyper Beam is super powerful. Manaphy is also shown to be hugged and cry 'Happy!' and 'Awesome!'
Badass Damsel: Let's summarize chapter 18 here: May attacks the Swordsmen with her Pokemon, demands a duel to bet her livelihood against Mai (and wins), proceeds to use Duel Monster Cards to escape, and taunts the group as she does. Then, she's at the rooftop....and that's where things get worse...
Badass Normal: While we don't know what the Goddess of Joy power up does, May is written as an exceptional duelist, able to stand toe to toe with any opponent she faces.
Bandage Babe: May becomes one after suffering knife wounds and blows from the Swordsmen. She keeps the bandages wrapped around her arms and torso and is told that she needs to change the bandages every few hours.
Barrier-Busting Blow: When Valon equips his Armor cards to himself outside of a duel, he's able to punch through doors and punch out an Egyptian God Card.
Bastard Boyfriend: Inverted. Raphael acts like one around May because of a combination of the Orichalcos and his lost memories. He also acts sweet as a ploy to lure May out.
Being Tortured Makes You Evil: Subverted with May. She gets tortured and tortured and tortured, and does gain a dark side, but her willpower is strong enough to make sure she doesn't give into the darkness.
Beta Couple: If there IS a main couple (what with Yami/Yugi and Tea being a focus—somewhat), it would be with May with either Raphael, Kaiba or Mokuba.
Beware the Nice Ones: Max and Mokuba aren't as fiery as May, but people should also be careful for them.
Max is the youngest of the Chosen, and pretty much cheerful. However, he also has Jirachi in Duel Monster form who is able to destroy one monster on the field for the cost of a Light monster in the hand. If Max tells Jirachi to use Doom Desire, he's pretty much wins the duel.
Mokuba is another offender of the trope. Innocent looking, but add the fact that He houses Khonsu, the Moon God, he's able to summon power to kick butt.
Calling the CEO Out: In the anime, Kaiba slams the phone after hearing Yami lose his duel. In the story, May remarks that Kaiba isn't doing anything and catches his insult in six words.
May: (to Kaiba) Yami's not the disgrace, you are!
Cassandra Truth: Raphael is unable to convince his fellow Swordsmen that May is this supposed savior he met on an island called, "Guardian of the Sea." It gets worse when May knows who he means—her ancestor—but Raphael is too stubborn to believe it.
Catch a Falling Star: May's Altaria saves her from a nasty death after an explosion knocks her off the Paradius building.
The Chase: Used in the second half of "Wrath of a Goddess." May's being chased by the Swordsmen so that she can escape.
Cerebus Syndrome: Subverted; the season was dark already...but then we added many of the below tropes...
Child Mage: Max is this, being the 'Prince of Wisdom' and all. He also wields a Spellcaster Deck (but also uses low Light attribute monsters like Golden Ladybug and Watapon).
Chekhov's Gun: May and Max are picking out booster packs and sharing cards. The cards they have will appear later on and help them in duels.
Remember the tag that Norman gave Max? It's a wishing tag, and it grants Kaiba the title of Regent of Wisdom when Max loses his soul.
The card necklaces May and Max make in episode 7? May uses hers in Wrath of a Goddess. Max doesn't use his but it's given to Mai to fend the Orichalcos Soldiers coming her way.
Cold-Blooded Torture: As if May didn't have to go through more abuse, when she finally is able to be safe from the Swordsmen, they somehow teleport to where she was at—Kaiba's jet—and a) act as if they don't remember their abuse (they don't) and b)plan on torturing her some more.
Cold Sniper: Penumbral Gunner, a Dark Monster said to represent Alister is described as this. He's also part cyborg.
Cool Big Sis: Inverted. Mokuba sees May as an older sister—despite him being around 11 or 12, and May being 10. This could be because he's enamored by the adventures she gets to go through.
Crazy Jealous Guy: Raphael and his ancestor are completely jealous of the Pharaoh for stealing their love away. In both situations, the Pharaoh is completely innocent, that is, if we are to believe what's being said in the story.
Cry into Chest: At the end of 'Beyond a Shadow of a Doubt', May does this to Kaiba after he says that things will get better.
Curb-Stomp Battle: Shadow's first duel is against Valon. It's a 3 turn duel with Valon unable to do anything when Psychic Armor Head—the card he needs the most for his deck—has been removed from play, and Shadow winning.
Cybernetics Eat Your Soul: Used with Penumbral Gunner, but it seems to be a representation of Alister's desire for violence and destruction. The appearance—an android with a face that's part human, part robot—seems to accentuate the importance of sacrificing human spirit for power.
Dark Is Not Evil: May utilizes two types of decks: a Gravekeeper's deck, and a deck that's comprised of most Dark monsters. She's also a good person and Goddess of Joy... most of the time, anyway.
The Dark Side: May unfortunately givers herself to the Orichalcos because she needed the strength to continue after her vicious pummeling. Subverted because she forces the Orichalcos out of her, if only temporary. Once she gets trapped, she gives in and unleashes her dark side.
Deal with the Devil: Deals with the Orichalcos are viewed by this. May went through one so she could be healed of her wounds. She also, unknowingly, released her darker side from the pact
Deconstruction: This story is not sunshine and buttercups. Characters involved in a crossover can't work together if they don't get along, the Secret Keeper can only hold so much information before being pressured, Reincarnation Romance can turn sour if one becomes obsessed with another who has no idea what's going on, being between Easily Forgiven to a Karma Houdini is very thin and the concept of Light is Good can come to light when your protagonist uses darkness as their aiding hand.
Deconstruction Crossover: The characters aren't getting along, and are not opening up to each other (Yugi and the others don't tell about Battle City, May and Max can't tell about Atem and his past), Pokemon are being subjected to monsters and power far worse than Team Rocket can do to them, and the characters are dealing with a world that will literally kill them without guilt.
Deconstruction Fic: This talks about what would happen if Dartz wanted his Swordsmen to attack people outside dueling, their mental states and how people would react to this whole ordeal.
Defeat Means Friendship: They were getting along well, but the duel between May and Mokuba ended with them laughing, shaking hands and cementing their friendship.
Despair Event Horizon: The ending of chapter 18 for May, the end of chapter 26 for Max, and the end of chapter 27 for Mokuba. This results in May falling to her doom, Max's soul gone and Mokuba has lost all of his monsters and Khonsu respectively.
Determinator: Max and May—despite being the youngest out of the main cast—show great skill in not giving up. It goes to the point that Max's first duel had him win while he still had 100 lifepoints left. and May stood up to Arkana using her old deck and defeated him.
Mokuba's time to shine was in his first Orichalcos duel. For someone who's never dueled before this story, he stands up to his opponent—Alister—gives him an amazing speech—and prompts that he will take the direct attack of 11,000 attack points and smile at his face while doing so, determined to make sure that the his loss would not be in vain.
Deus ex Machina: Deconstructed. What turns out to be a blessing in disguise A fake Winged Dragon of Ra winds up into May and Max's hands, actually becomes a horrible thing as it unravels everything that came before and after it. Because of this, May gets horribly beaten and chased for having the real Ra in her possession.
Duels Decide Everything: Deconstructed. Just because they can decide everything doesn't mean it's successful. Yami's duel with Yugi only makes May lose trust with Ironheart and Chris, stating that they had no idea how much it hurt Yami.
Disproportionate Retribution: Shadow inflicts punishment to Valon this way. Valon also does this when he punches and attacks May for winning against Mai in an Orichalcos duel. Shadow's punishment involves calling out the names of the Armor cards in Valon's deck, while Valon feels pain the particular area. After she goes through every monster, she stabs his heart with a dagger...a dagger that takes people into their worst fears.
Easily Forgiven: Deconstructed. The story talks about how much it would take to actually forgive people of their crimes. May has the most trouble, seeing as she's been sliced, hacked, punched and broken by the Swordsmen who were brainwashed. She's having trouble on whether it was truly their fault or not.
Soul Power: Mokuba has this by having a spirit by his side, using monsters based on stars, and creating barriers.
The Empath: May is noted to sense and understand the hearts of evil and can see from their perspective. However, if she doesn't know a lot about a person, she can't really help them. It's also Deconstructed because despite understanding people, she just can't understand how to feel about them since she's so confused about what she's feeling from them.
Even Evil Has Loved Ones: The Swordsmen all have lost people in tragedies planted by Dartz; of course, this is taken to newer heights for Raphael seeing as his loved one is the one who is trying to stop the Orichalcos from destroying the world.
Even Kaiba Has Standards: Kaiba is known to be cold to everyone but his little brother but he showed disgust and shock in finding out about the torture May went through. This makes him decide to fight with Yugi and the others cause that means that the Swordsmen were going to hurt more innocent people.
Fate Worse Than Death: Do you want to die? Of course you do when you're trapped in a realm that makes you relive your biggest fear over and over by a dagger driven into your heart! The worst part is that the it might be permanent if the owner of the dagger doesn't reverse the damage.
May even points out that she'd rather die than be a captive to Raphael. For the record, she does get captured.
Faux Action Girl: Inverted. May is told to run away when she says she can handle a duel on her own. The only reason that she doesn't fight is because of many things. First off, she has the Winged Dragon of Ra on her, and that's what's needed to strengthen Leviathan. Second, Raphael wants her and she needs to run off before he does something...awful to her. Last, even if she is the Goddess of Joy, she has no magic power that she can use to defend herself.
Feather Motif: Played straight with May and Mai. While Mai is the Broken Harpie with her Harpie Ladies, May also has feathered friends. One of her dark monsters is Dark Horus who sports black feathery wings, and she also has her Altaria, with white cloudy feather wings. Dark Horus represents that even when using Dark Monsters she can still be good, Altaria represents her gentle spirit as the Goddess of Joy.
Flashback: The story only uses it them around Raphael whenever he gains visions of his past life as Rael, and his interactions with Hara, May's ancestor. Unfortunately, these are only fragments, so he doesn't understand what's the real story.
Forced To Watch: Max and Mokuba aren't forced to watch May being tortured, but they're being forced to watch May break down from her wounds and torture.
Foreshadowing: May falls off of the scaffolding of a building in chapter 4 by Raphael. In "Wrath of a Goddess"—14 chapters later— the same thing happens, except there's an explosion this time. In both times, her Altaria saves her from becoming a bloody pulp.
Four is Death: All over the place. Many of May's Dark Monsters are Level Four, she has four main duels before the explosion at Paradius, Max won four duels— the fifth duel had him lose his soul—Mokuba has also won four duels before he lost all of his monsters and Khonsu four chapters later, four duels with revived Orichalcos warriors appear between chapters 24 and 28 (four chapters, etc.
From Bad to Worse: It did starting at around the end of the chapter entitled 'The Wrath of a Goddess.'
Genki Girl: May shows signs of this, as she's excited to go save the world. Then chapter 18 happens...
Girl in Black: May's dark side Shadow is this, with a dark attitude to match.
Girl with Psycho Weapon: Shadow keeps a dagger on her...that said dagger is able to transport people into a realm of their worst fears without any hope of escape.
Glass Cannon: May when using her Gravekeepers Deck. They're pretty strong, but they have to rely on Necrovalley or Gravekeepers Priestess to keep them on the field. Also, her strongest Gravekeeper doesn't go past the 2,000 Attack Point mark, so if Gravekeeper's Visionary is destroyed, she's pretty much a sitting duck.
Although that's if she only has Gravekeeper's. Her main deck is much more balanced that she can use its diversity to fight back.
Glowing Eyes of Doom: Happens in the second half of the story. People who were defeated in Orichalcos duels return, their eyes glowing green to symbolize the Orichalcos taking control
God in Human Form: Averted. Hara, Guardian of the Sea, is NOT the Guardian of the Sea. She's just a girl playing make-believe. That doesn't stop Rael from believing that and to keep calling her that.
Go Out with a Smile: Mokuba does this in chapter 24... He gets better.. Deconstructed because he doesn't realize how his going out is affecting people who care about him, and tearfully cries an "I'm sorry" after it's all over.
Graceful Loser: Those who have been revived by the Orichalcos and come to their senses, become this. They thank their opponents from freeing them from the influence of the Orichalcos and begged them to finish them off.
Hates Being Touched: Subverted with May. She'll accept a hug, but she freezes when someone grabs her wrist.
Healing Hands: If this is to go by, Max can temporary stop pain caused by sensing darkness, and May could be able to heal souls of upset emotions. We're not sure about Mokuba though.
Hoist by His Own Petard: Alister talks about peace and how Dartz would end all wars. In a very ironic twist of fate, his strongest monster attacks with war weapons. How is he defeated? When his attack is stopped by a trap card that's called 'Sign of Peace'.
Mai also ends up like this. In her duels, she constantly uses 'Harpie Lady Phoenix Formation' to destroy all of her opponent's lifepoints She loses monsters against May when she used Manaphy's special effect. To top it all off, May used a monster that could destroy all cards on Mai's side of the field by removing from play one card. Ironically, the monster gives the opponent lifepoints for every card that was destroyed....then Mai loses them anyway when May attacks directly.
Hope Spot: It goes horribly bad. Just when May has finally escaped the Swordsmen they arrive while she is trying to contact help, and then pin her onto the ground. Did we mention that she's on a jet when this happens?
Hostage for MacGuffin: Raphael makes a deal for Yugi's soul: He'd give it back for the Winged Dragon of Ra. Of course, the protagonists won't give the card, so he goes for the next best thing: May.
Hurting Hero: May was a cheerful Pokemon Coordinator, Max was a cheerful kid with lots of knowledge, and Mokuba was the younger brother of a CEO before chapter 17 happened. Then when that was resolved May becomes scarred with a dark spirit inside her, Max loses his soul and Mokuba has basically lost most of his powers...all in one day.
Imaginary Friend: Deconstructed. Atem notes that he and the others were so real to May, that she was willing to use a ritual—at age 7 to make them become rela. Said ritual involved cutting her arms and using her blood. No wonder the mom didn't like it. One has to wonder what May's mental state was at the time.
Improvised Weapon: May will utilize Duel Monster Cards to get the heck out any situation she's in.
Indy Ploy: May's attempt to escape Paradius. All she does is keep running and summon Duel Monster cards to stall the Swordsmen from capturing her.
Infant Immortality: Averted. May, Max and Mokuba are targeted by the big bad and each have suffered various wounds for children their age.
What's even worse is that May and Mokuba's ancesetors died when they were young (at ages 10 and 7 respectively)
In Medias Res: Chapter 26 ends with Raphael about to stab May in the back with a knife and Chapter 27 begins with Mokuba unconscious and the story picks up as to how it happened.
Innocence Lost: May, Max and Mokuba go through hell in one single week, seeing destruction and darkness everywhere.
Insistent Terminology: Inverted. Atem knows the names of the Chosen, but he always refers to them by their titles. This commonly occurs to May as he always calls her 'Goddess of Joy' instead of her real name. And even if he doesn't state their names, he'll call Max 'your brother' to May.
Instant Expert: Averted. Since the chosen only got their powers recently—and are being chased by madmen wherever they go—they never get the chance to actually train their abilities.
I See Dead People: May, Max and Mokuba are all able to see Atem and other Duel Monster Spirits, but May is the one who was the first to have this ability.
It's All My Fault: Poor, poor May. In trying to stop Leviathan from being destroyed, she caused a LOT of problems.
I Want Them Alive: Deconstructed again. The Swordsmen will beat the Chosen into an inch of their lives, but they'll keep them alive long enough for Dartz to take their souls. This also has a bad effect on May, who is in constant worry that the Swordsmen will come out to beat her up.
I Will Find You: Deconstructed. Raphael becomes obsessed with finding his Guardian of the Sea, to the point that Valon and Alister are actually annoyed by this, his mental state is completely fucked up, and the person he's finding is getting harmed by his thoughts of being together with him.
Jack Of All Trades: Out of the three chosen, this is Max. Although he has the most Magic cards, he balances this out with the effects of his monsters and traps to keep opponents at bay.
Jerk with a Heart of Gold: Kaiba shows his side to May when he bandages her wounds. May even replies with a thank you for the act.
Kid Hero: Deconstructed. The only things that are keeping these kids alive are victories over duels and Pokemon battles, and they have barely little training in what they're supposed to be doing as Chosen (it took May close to the end of the story to pull out a Magic Music moment).
Kick Them While They Are Down: Valon does this to May. Why? Because she dueled Mai under the Orichalcos and defeated her, thus Mai's soul was sealed away.
Kill The Ones You Love: According to May, her ancestor died because Atem killed her with a stab to the heart. Granted, this was because he was corrupted by a dark evil in his heart, but it still counts.
Knife Nut: Raphael has his trusty knife hidden in his boot—which was cut from the 4Kids dub—which he'll use to kill anyone in his path and stab/slice a girl to pieces.
Shadow keeps a dagger on her.
Lightning Bruiser: In terms of dueling, this is Mokuba. His strongest monster has 4,000 Attack Points, but his diversity in Monster cards makes sure that he doesn't have to rely on him too often. The downside is that he's not that great when it comes to using Trap cards.
Love Makes You Crazy: Valon would beat up a girl for making her lose Mai's soul. Raphael's crazy due to emotions and the Orichalcos, and Alister's love for his brother would make him want to destroy the world.
Love Makes You Evil: Raphael goes into this in the story. Instead of deciding that the world needs to be cleansed, he wants it to be cleansed AND makes sure the love of his life is with him. Has it been mentioned that the love of his life is only 10?
Mad Oracle: Subverted. Jouno isn't particularly mad, just quiet. However, since we haven't heard about his past, one can assume that just because he's silent, it doesn't mean he hasn't been traumatized.
Magic Knight: From what we're given so far, Mokuba could count. He's learning some magic with Khonsu, and his weapon is a giant curved blade.
Magic Music: May notes that Hara loved singing. Given that she may—or may not be—the Guardian of the Sea, she might have some power.
May has this power as of the latest chapter. She sang a song to Raphael that seemed to make him calm down...instead, it did the opposite. It made him more obsessed with her.
Magic Wand: Max has one topped with a wand, and May has a sistrum.
Make a Wish: Jirachi, the Wish Pokemon makes an appearance in the story, being the guardian Pokemon of Max. With a single wish he was able to find help for May, and granted Kaiba the powers of the Prince of Wisdom when Max lost his soul to the Orichalcos.
Making a Splash: May has two monsters in her deck that are Water types. Both monsters help secure victory in the duels they debut in.
May-December Romance: Deconstructed. Raphael is at least in his 20's, and May is 10 years old. Raphael is obsessed with her only because she looks like his supposed savior. May, naturally, doesn't understand what is going on and is freaked out at the whole idea. Still, it doesn't stop Raphael from continuing to pursue a lover at least half his age.
Mental World: Playing with the soul room idea, Mokuba has his own. Mokuba's soul room is pretty plain, but covered with stuffed animals, representing not only his innocence, but also his loneliness.
Misery Builds Character: Deconstructed. Sure the misery that affects the chosen builds character, but it's not the correct type of character. May's pretty much strained between forgiving people who hurt her, Mokuba blames himself for letting May get hurt, and Max is divided as to how all of this plays out.
Mistaken Message: Hara confused 'like' for 'love'... cut to about 5 millennia and that's being taken the same way with Raphael and May.
My Name Is Inigo Montoya: Mokuba does this just as he's about to die—emphasize die—by lasers and missiles from Alister's monster.
Mokuba: (to Alister) My name is Mokuba and I choose to be your sacrifice for your brother, Alister! Hit me with your best shot!
Outrun the Fireball: May has to outrun one she made. She summoned Exploder Dragon to deal with Raphael's Guardian Ceal. The results? An explosion May is running away from BEFORE it starts and her escaping just in time.
Plucky Girl: May embodies this trope until her trauma after Wrath of a Goddess. Then she gets it back, but the following chapters are slowly making her break.
Power Trio: May is Superego, Max is Id and Mokuba is plain Ego.
Prophet Eyes: Khonsu has them to represent his powers of the moon. Mokuba also wears them whenever he lets Khonsu take control.
Psychic Powers: Jouno has precognition, and Raphael has some type of postcognition, May shows signs of empathy, and Mokuba has bits of clairvoyance in him. The Chosen have bits of telepathy by communicating with their Duel Monster spirits. Unfortunately, they aren't sunshine and buttercups as the Blessed with Suck trope tells us.
Pursued Protagonist: Halfway through 'Wrath of a Goddess', May's being pursued because she has the Winged Dragon of Ra. She's not killed, but the wounds she received aren't going to heal so easily.
However, it's deconstructed. It absolutely sucks.
Red Eyes, Take Warning: All users of the Orichalcos have this whenever the Seal is played. May receives this whenever Shadow takes control.
Kaiba temporarily had them when Shadow awakened his own darkness.
Ritual Magic: Mokuba goes through this when he first gains his powers.
Royals Who Actually Do Something: The three chosen—May, Max and Mokuba—have different titles (Goddess of Joy, Prince of Wisdom, and Defender of the King, respectively.). Despite their age, the three children participate in duels and fight in the front line, rather than sit back and let other people do their dirty work.
Rule of Three: There are three chosen (May, Max and Mokuba), Max gets three Pokemon on his journeys Banette, Vigoroth and Absol, Mokuba's competed in three duels (as of the latest chapter) and May and Max fight against trainers using three Pokemon]].
Secret Keeper: May, Max and Mokuba were promised not to tell Yami about his past. If they get questioned about it, people start to suspect something is wrong.
It's also deconstructed; they aren't the only ones with the secret. May has to constantly ask what exactly happened in Battle City and never gets an answer. The secrets slowly cause them to not trust in one another.
Self-Fulfilling Prophecy: Jouno is able to predict the future. However, the future turns out to be very bad, and always happens. This doesn't stop the protagonists who see his visions try their hardest to avert the fate.
Two of them are based on the film The Iron Giant. First is Alister's strongest Duel Monster which is described to look like the titular giant but also has red eyes and powerful weapons. The second is Mokuba's speech toward Alister which states, "You are who you choose to be."
Many of Max's later cards have this. For example 'Sorcerer's Assistant-Miey' is actually based on Mickey Mouse from The Sorcerer's Apprentice. (she even has her hair styled like Mickey Mouse ears and a red robe, but she doesn't have the infamous hat)
Shown Their Work: The author knows the series well, referencing stuff from the manga, the anime and researching cards (well, except for one). Many of the created cards were researched and based upon different works. Also during the scene where Kaiba is bandaging some of May's wounds, the author goes to great lengths to reveal how to bandage the bruises.
Spirit Advisor: Khonsu, the God of the Moon, is this to Mokuba. However he's not shown doing a lot. This could be justified as saying that this is mostly Mokuba's chance to stand up and not be on the sidelines, and Khonsu guiding him. (That and since Khonsu is a god, he'd pretty much be doing all the beatings)
Stuff Blowing Up: In "Wrath of a Goddess", there are five sets of explosions all based on Duel Monster cards.
Summon Magic: The Chosen have this, but May gets bonus points for summoning the Winged Dragon of Ra into the real world.
Tears of Joy: When May finds out Manaphy is alive these are shed.
Tears of Remorse: Mokuba sheds these once he realizes that by winning an Orichalcos duel against Alister, Alister's soul is sealed away. It gets even more heartbreaking when one realizes that he originally was going to lose the duel from a direct attack.
Throwing Down the Gauntlet: Before May challenges Mai to a duel, she decides it's best to prove that she wants out of the place she's in Paradius by unleashing all 6 of her Pokemon to kick everyone's asses.
Torture Always Works: Sure, let's torture the person that's given us a living hell, and then let's beg for mercy in about 4 chapters when said person decides to get her revenge!
Up to Eleven: You know the whole thing about monsters in tablets and then the Duel Monster thing? This puts in the situation of spirits of Ancient Egyptians and even STARS to become Duel Monster Cards.
WHAM Episode: Wrath of a Goddess and Beyond a Shadow of a Doubt are contenders for this.
White Magic: Max can heal—somewhat—and Mokuba's title is 'Defender of the King', hinting that he can create barriers or use defensive magic.
The Wise Prince: Inverted. Max, the Prince of Wisdom, has gained the respect of Dark Magician, stood up and sacrificed himself to the Orichalcos, and very knowledgeable about Pokemon. He's also seven years old.
Would Hurt a Child: They would. There were actually threats made by Alister that the Swordsmen would hurt Max if May didn't return the Winged Dragon of Ra to them. It should also be noted that Alister gets to duel a Kaiba and plans to destroy said Kaiba with a monster 11,000 attack points. Said monster attacks with lasers and missiles.
It gets worse. Max's first duel was against Arkana. The kid goes through a direct attack that hits him for around 5100 damage. Then he gets attacked by ectoplasm; he's only 7.
What about Ancient Egypt? Hara and Moka were killed at very young ages.
Would Hit a Girl: Oh they would. The Swordsmen slashed May's arms front and back, and punched her to the point that her ribs would crack. They also have used knives to silence her, pin her to the ground or wall, and just wail on her.
Yandere: Raphael is a male version of this, Shadow plays it straight with Kaiba.
Yank the Dog's Chain: May's safe from harm, that's awesome! She's gonna see if Kaiba's won his duel and...wait...who's choking her?!
You Said You Would Let Them Go: Inverted. After May finishes her duel against Mai, she asks Dartz to release Yugi's soul as part of the deal. Dartz says he can't because May NEVER made a deal in question. She only asked for a way out.