The Alcoholic: The Sage of Duelists is a recovering one. Like most people who had this sickness, it cost him almost everything until he was helped by the former Sage. In the fic, his deck uses mostly anime-only liquor-related cards, both to remind him of the addiction he used to have and to prove that he controls it, not the other way around.
All Myths Are True: Fortunado obtains an artifact called the Scepter of Bound Divinity which allows him to free divine beings who got in trouble with their superiors and at least point them in the right direction to cause trouble. He is thus able to free Loki and Eris so that they can challenge the protagonists. (This fic was written long before a card was made based on Loki.) He also attempts to do the same with Kali, but she is locked away too tightly, and only summons a worshiper who tries - and fails - to finish the job.
The protagonists also meet Athena, who arrives to haul Eris away again once she is defeated.
Artifact of Doom: The Seal of Orichalcos. In this fic, its evil power is even greater, as it lays a curse on the soul of anyone who uses it. The curse can be lifted, however, and many users, including Mai, Weevil, and Rex were saved from this fate. Raphael, Valon, and Alister were not so lucky, but their curse is lifted halfway through the story by the heroes.
Back from the Dead: Panik, Espa Roba, The Paradox Brothers, Rex Raptor, Weevil Underwood, Bandit Keith, Lumis, Umbra, and Yami Bakura.
Bad Moon Rising: An unscheduled total lunar eclipse indicating that the final battle of the Reckoning is about to begin.
Balance Between Good and Evil: The Balance, a sort of celestial detente between the four powers of Light, Darkness, Dreams, and Shadows, created to ward off the power of Chaos. Its champion is the Dark Messiah.
Blindfolded Vision: Jason. Once he receives the power of the Dark Messiah, his eyes turn golden. Since as the Dark Messiah Jason has inward sight, he puts on the blindfold to keep people from freaking out.
"Feh," said Loki, drawing five cards. "Feel free to make the first move. It really doesn't matter. I haven't been outwitted in a game of skill since the founding of Asgard."
"And when was that?" asked Ben, drawing a sixth card.
"I think it was on a Tuesday," answered Loki. "Very few people know that!"
Call Back: During the final battle, Jason uses the Dark Messiah's effect to banish Marauding Captain, Nanobreaker, and Vorse Raider to power himself up. Those three each lead Russel, Trisha, and himself to Hermos, Critias, and Timaus respectivly.
Continuity Cameo: Panik, Espa Roba, The Paradox Brothers, Rex Raptor, Weevil Underwood, Bandit Keith, Lumis, Umbra, and Yami Bakura.
Corrupt Politician: The mayor of New York is Sin in disguise. When presented with this fact, Russell is hardly surprised; as he says, "Like my dad said, ever since Teddy Roosevelt, there has never been a good politician."
Deal with the Devil: Fortunado to Sin. By working for her he gets a front row seat to the Reckoning, and can make a documentary of it.
Sin actually uses a card called Faustian Pact. It's Exactly What It Says on the Tin: With the pact active, she gets to summon the servants of the Nine Lords of hell, but if she loses after using it, they get her soul.
Dragon Rider: Shining Dragon Knight, the result of Timaus being used on Blade Knight.
Fanboy: Jason is one of Seto Kaiba and as a result, based his deck of Kaiba's, minus the Blue-Eyes White Dragons. He sometimes fantasizes about owning the 3 Blue-Eyes cards. And at the end of the fic, he does.
Heroic Sacrifice: Sin offers Cassius, Sebation, and Cleo a second chance to duel Russell and Trisha in a tag team duel. She makes Cassius choose which member of the trio gets to stay in her stomach. Cassius chooses himself.
Hoist by His Own Petard: Fortunado almost tricks Jason into using Cyber Laser Dragon's effect on his White Knight Lord, thus winning the duel. His overacting gave it away, and Jazon zaps Fortunado's Jinzo instead.
The Puppeteer of Death is nearly defeated this way too in his second duel with Russell. He tries to use the exact same trick that he used to win the first duel, not realizing that Russell is more than prepared for it this time (and actually hoping he'll do it). This doesn't cause him to lose right away, but it forces him to make risks that he didn't plan to, and is dealt a crushing defeat at the end.
Homage: The setting is a Duel Academy, similar to the one in Yu-Gi-Oh! GX. Like the school in that series, the students have three rankings, Slifer Red, Ra Yellow, and Obelisk Blue. Unlike the old one, you cannot start at a high rank. Everyone (girls included) start at Slifer and are promoted based on merit. Students know rumors of a fourth, higher rank called Exodia Gold, but it is not confirmed. Exodia Gold is an exclusive club for duelists who have gone above and beyond the call of duty, and membership is by invitation-only. One of the requirements for entry is to survive a Shadow Duel.
Another example was that Melissa Etheridge's "I Run For Life" was used as an introduction to the first chapter (although the word "duel" was used to replace "run", so it may have technically been a Song Parody.)
Horny Devils: Namia, the Erines Queen. A Archdevil used by Sin, any monster she battles while she is in Attack Mode becomes brainwashed and Namia's controller (Sin) gains control of the other monster. To make things worse, when she makes a direct attack, she kisses the duelist.
Large Ham: Fortunado. He was a movie producer. (When Jason expresses doubt at this, he says, "Fine, I'm an evil businessman from Los Angeles, which is basically the same thing.")
Masquerade Ball: The Academy holds one, on Halloween naturally. Dark Magician Girl - as in the Duel Spirit - shows up, and after a frivilous exchange, gives some important information to the protagonists.
Meaningful Name: A family tradition of Malvolio's family names all male members after Shakespearian characters. ("Malvolio" is a character in Twelfth Night.)
No Sell: Double Pinaska's effect allows him to stop any one attack towards anything (himself, another monster, even a direct attack), yet he can only do so once a duel.
Obfuscating Insanity: Malvolio Lark is one of the most eccentric students in the school... and hasn't failed a single assignment. In truth, he's the descendent of one of the greatest duelists in American history, but after constantly being challenged to duels over his family reputation, he started acting crazy just to keep everyone away.
Old Master: The Sage of Duelists, a mysterious sensei who runs a monastery in the bowels of the city where he trains duelists to communicate with Duel Spirits including Chazz Princeton, Alexis Rhodes, Tyranno Hassleberry, and Aster Phoenix, who remain eternally young due to a wish they made to be duelists forever. He has strange powers, and has been waiting a long time for the Reckoning. He is the one who bestows the power of the Dark Messiah upon Jason.
One Curse Limit: Anybody who uses the Seal of Orichalcos will wander the Earth as a ghost unable to pass on after they die unless they have special protection. When it is pointed out Yami Yugi used it before, it is explained that Yami was already under the curse that erased his memories and bound him to the Millennium Puzzle.
Our Zombies Are Different: Penelope, the Lady of the Night. Although she is a Zombie, she is a Light attribute monster, and a Card of Virtue.
In the original draft, it was Vampire Princess Miyu. But then Cyber Commander was tipped off as to where the name came from (the card was a Contest Winner Cameo, so he wasn't the one who'd named it) and renamed it to avoid accusation of plagiarism.
Prisoner Exchange: After a member of Fortunado's gang is captured by the school's headmaster(which would be bad for him, as he might talk) a very grim version of this occurs. Sersei is challenged to an Orichalcos Duel and loses, and the villains demand the prisoner's release in exchange for her soul. The headmaster agrees, and while the villains do keep their word, it leads to another Orichalcos Duel involving Jason (which, incidentally, is where Jason is chosen by Timaeus, the first Legendary Knight to appear.)
Power at a Price: Jason must give up his physical sight in order to gain the power of the Dark Messiah. He at first believes this is permanent, but after defeating Sin, he is told that it was a "collateral", done to make sure that the power was not abused or used for selfish purposes.
Powers That Be: The plot of the story revolves around an event demanded by higher powers called The Reckoning that happens once every thousand years. In this event the forces of Good and Evil, respectively, choose mortal champions in a competition (if not a war) in an effort to decide which moral philosophy is superior. Evil has a very poor track record in these contests, and the side of Evil is becoming increasingly worried that a permanent ruling in the favor of Good might eventually result. As it becomes time for it to happen again, Sin has decided to take drastic measures to ensure that the tide turns.
Recruit Teenagers with Attitude: Inspired by the Sage of Duelist's word that [Good has] many allegiances and allies, but Evil always stands alone." The protagonists decide to launch a preemptive strike on Fortunado's stronghold rather than wait for him to bring the fight to them. This means raising a sizable force, and they get many volunteers from the students at the school.
Robot Buddy: Dr. Artemis has a robot assistant named Twinky.
Screw the Rules, I Have Supernatural Powers!: The Seal of Orichalcos is a broken card at best; Sin uses it in a way that is outright cheating. She does not need the card itself to generate it, able to project it from her body, can activate it during her opponent's turn, and even have it active while another Field Spell is in play.
Secret Weapon: Raviel, Lord of Phantasms, used by the Puppeteer of Death. The card is actually a counterfeit, and there are plans to create counterfeits of the other Sacred Beasts, but Russel destroys the card, ruining those plans.
Seven Deadly Sins: Cursed Spell Cards are created to work specifically with The Seal of Orichalcos, each one corresponding to a specific one of the Deadly Sins. The more a user indulges in the sin, the more likely he is able to use it properly.
Seven Heavenly Virtues: To even the playing field, Spell Cards are also created based on these concepts and given to the heroes and those who volunteer to fight the Orichalcos.
Shout-Out: Xinothium, the incredible unstable and volatile fuel that powered the Red X suit in Teen Titans, also makes an appearance in one chapter, where it is the power source for a sentient computer.
Stone Wall: Dr. Artemis's deck, which she describes as a Jujutsu Deck.
Soul Jar: Whoever loses a duel where the Seal of Orichalcos is used has his soul consumed by Sin, and is kept prisoner inside her. She is able to communicate with them, and can actually cause them pain. Usually, however, those who are released (often after being used as a bargaining chip) can only recall isolation and darkness. It is implied by some members of the organization that is is possible for captive souls to be truly eradicated, but because she does not do this, it may not be true.
The Chosen One: Like the first time the Orichalcos was a threat, Timaeus, Hermos, and Critias appear and bestow their blessings on the three main characters. Unlike last time, they appear in human form the first time they appear, but as dragons most other times. (And as their card's effect show, they haven't lost their touch.)
Jason is a special Chosen One, as he is given the mantle of the Dark Messiah, the one who is to fight the final battle of the Reckoning. Cyber Commander actually held a poll beforehand to determine which of the three main protagonists would gain this title.
Unexpected Character: While many of the Cameo characters might have come as little surprise, the Puppeteer of Death (who was actually an important villain in the fic) might have been much more unexpected. This obscure Yu-Gi-Oh character only appeared in the manga (he was replaced by Ghost Kaiba in the anime) and even to fans of the manga, wasn't the most memorable villain.
Throw the Dog a Bone: When Rex shows up, he mentions that Weevil has subscribed to the rules for redemption laid out before him and has escaped the purgatory Rex is stuck in. Cyber Commander added this section after being told he'd treated Weevil far too harshly in previous stories.
Timed Mission: Each chapter begins and ends with the time and date to show a countdown to the climax, where the final preordained battle is to begin. (See Bad Moon Rising.)