Chapter 1: Dawn of a New Era Part 1
Ten years have passed since the Ceremonial Battle and now it's time for the next generation of duelists to shine. Jaden and Reyna Yuki are both candidates to enter the prestigious main branch of Seto Kaiba's Duel Academy. Reyna is thre on time, while her brother is not so on time.
Chapter 2: Dawn of a New Era Part 2
Jaden's duel to see if he gets into the academy is next! He ends up facing Vellian Crowler, one of Duel Academy's professors, in a Duel to gain entrance to the Academy
Chapter 3: Welcome to Duel Academy!
Jaden, Reyna, and the other First Years have arrived to Duel Academy!
Chapter 4: Obelisk vs. Obelisk!
Reyna duel against Chazz Princeton's lackey, Raziou.
Chapter 5: Duel for Love? Say What?!
Dr. Crowler attempts to get Jaden Yuki expelled from Duel Academy, but instead catches Syrus Truesdale in his trap. Jaden duels Alexis Rhodes, with Alexis agreeing to remain silent about Syrus' trespassing in the girl's dorm if he wins.
Chapter 6: Dragons vs. Heroes
Reyna meets Obelisk Blue's Dragon Queen, Reika Tsumura, who challenges her to a duel! Will Reyna survive against her?
Chapter 7: Promotion Drama!
The Duel Academy Promotion Exams are here!
Chapter 8: Return of the Shadow Games Part 1
Jaden, Reyna, Syrus and Chumley learn of the Abandon Dorm. After getting separated from her brother, Reyna finds a room full of profiles and one catches her attention.
Chapter 9: Return of the Shadow Games Part 2
Jaden faces off against Titan, a Duelist hired by Dr. Crowler to scare Jaden away from Duel Academy, and one claiming to be able to initiate Shadow Games.
Chapter 10: Return of the Shadow Games Part 3
While Jaden duels Titan, Reyna is up against someone called the Shadows.
Chapter 11: We’re WHAT?!
Jaden, Reyna and Syrus are punished for their trespassing at the Abandoned Dorm, and a duel is set up. If they lose, they'll be expelled, but if they win, they'll get off with no punishment. Reyna duels agaisnt Alexis and Jaden and Syrus Duel against one another as practice, and the latter's self-esteem issues interfere with his Dueling.
Chapter 12: The Duel for Syrus
In order to help Syrus overcome his mental block about using Power Bond, Jaden Duels Syrus' older brother Zane, widely known as the best Duelist at Duel Academy.
Chapter 13: Family Matters
Chumley Huffington's father wishes to pull him from Duel Academy, believing him to be a failure as a Duelist. He intends for Chumley to work for the family business and give up Dueling.
Chapter 14: Judgment Duel: The Puppet
Reyna is first for her Expulsion duel and she' up against a Pro who can take control of her monsters.
Chapter 15: Judgement Duel: Paradox Trouble
Jaden and Syrus face their punishment for trespassing at the Abandoned Dorm - a Tag Duel against the Paradox Brothers, and if Jaden and Syrus lose, both of them will be expelled from Duel Academy.
Chapter 16: Equation for Success
Bastion Misawa and Chazz Princeton prepare for a Duel against one another, with Chazz's seat in Obelisk Blue on the line. At the same time, both Bastion's friendship and rivalry with Jaden Yuki deepen. In addition, Reyna duels to get into Obelisk. Will she be able to win?
Chapter 17: Miss Duel Academy
Chapter 18: Ape Escape
Chazz leaves Duel Academy, and in attempting to find him, Jaden discovers men from an animal testing lab deep in the forests around Duel Academy. He Duels one of their "creations", a monkey named Wheeler.
Chapter 19: Spirit Game
When three Obelisks manage to summon the Spirit of Jinzo, Jaden must duel Jinzo in order to save them.
Chapter 20: Christmas Holiday
Chapter 21: The Courtships
Jaden ends up in a duel against Harrington Rosewood, a third year Obelisk Blue student who is in love with Alexis Rhodes and mistakes Jaden and her for a couple. In addition, he must duel someone that likes his sister!
Chapter 22: The Dueling Giant and the Spellcaster
Jaden, Syrus, Reyna, and Chumley, head into the dead of night to find the mysterious Duel Giant. During the hunt, they run into Reika and use her to gain the Duel Giant's attention. After defeating the Duel Giant, Reyna and Reika run into an Obelisk Blue named Yoshiro Yukimura.
Chapter 23: The Eggwich Thief!
Jaden tracks down and Duels Damon, a former student who has been breaking into the card shop and stealing the Golden Eggwich each day.
Chapter 24: The Copy Cat King!
An exhibition featuring Yugi Muto's Deck arrives at Duel Academy, but before it can officially be displayed, it is stolen! Jaden and friends search and find the thief: a Ra Yellow named Dimitri. In order to get the Deck back, Jaden duels him.
Chapter 25: The Maiden and the Elementalist
Two new transfers, Blair Flannigan and Mei-Xing Li, arrive at the Slifer Red dorm. Reika soon finds something fishy about Blair and learns that he is not who he appears to be. When Jaden finds about Blair's secret, he duels him.
Chapter 26: The Duel Off: Part 1: Genius vs. The Hero
Jaden is pitted against Bastion in a Duel to determine which of them will represent Duel Academy in the inter-school match against North Academy. At the same time, a reporter named Gerard arrives on the island, and goes undercover to gather information about the Abandoned Dorm.
Chapter 27: The Duel Off: Part 2: Harpies vs Elemental Dragons
After Jaden and Bastion's duel, it's niow time for Era and Mei-Xing to go face-to-face.
Chapter 28: The Duel Off: Part 3: Brother vs. Sister!
The final duel to decide who will represent Duel Academy in the School Duel is here! It's Brother vs. Sister! Hero vs Hero! Who will win?
Chapter 29: The Mokey, Mokey Duelist!
Jaden is forced to duel Belowski, a former Obelisk Blue student who was isolated from the rest of Duel Academy due to his strange powers. Dr. Crowler hopes that Belowski's powers will rid Jaden of his motivation to Duel, thus disallowing him from participating in the Duel against North Academy's representative.
Chapter 30: Rise of the New Chazz
After leaving Duel Academy, Chazz Princeton ultimately ends up outside the gates of North Academy, while losing his Deck in the process. Using a new Deck constructed from cards around the surrounding area, Chazz enters North Academy, with the goal of becoming its top student.
Chapter 31: The School Duel
The inter-school match between Duel Academy and North Academy begins, with the school's representatives of Jaden Yuki and Chazz Princeton renewing their former rivalry.
Chapter 32: Gravekeeper's Challenge Part 1
Jaden, Reyna, Syrus, Era, Alexis, and Chumley, plus Reika and Professor Banner, have a field trip to the Academy's Ancient ruins. But their field trip turns into a life threatening duel! Jaden as to duel the Gravekeeper's Chief in order to save Syrus, Chumley and Professor Banner!
Chapter 33: Gravekeeper's Challenge Part 2
While her brother duels the Chief, Reyna has to duel the Gravekeeper's Priestess in order to save Era and Alexis!
Chapter 34: Gravekeeper's Challenge Part 3
After getting separated from the Yuki twins, Reika finds herself in a duel against the Gravekeeper's Heretic who claims that she stole something!
Chapter 35: Protect the Sacred Beasts!
Jaden is up against the first of the Shadow Riders: Nightshroud and must duel to save Syrus and Chumley!
Chapter 36: Attack of the Red-Eyes!
Jaden's duel with Nightshroud continues.
Chapter 37: Plants Come to Life
When Nightshroud fails, the second Shadow Rider, Dark Rose comes!
Chapter 38: Vampire Attack: Reika’s Challenge
The third Shadow Rider, a vampire named Camula, is next. And this time Reika duels her!
Chapter 39: Vampire Attack: Zane’s Revenge
In an effort to end Camula's crusade, Zane steps forward to Duel her. He dominates the early Duel, but is soon faced with a decision in which he is forced to balance the worth of his own soul against that of his brother's.
Chapter 40: Vampire Attack: Jaden Strikes Back!
Two of the Spirit Keys have been lost to the Shadow Riders, thanks to Camula, and Jaden Yuki is next to challenge the vampiress. With some advice from Atticus Rhodes and help from the Shadow Charm of the former Gravekeeper's Chief, Jaden must rally his Elemental Heroes to victory by summoning a new Elemental Hero to defeat Camula's Vampire Genesis.
Chapter 41: Into the Spider’s Web Part 1
The fourth Shadow Rider makes his appearance, but Reika finds something familiar about him and duels him even though she already lost her key! Will she and her dragons be able to go up against Black Arachnid and his army of spiders?
Chapter 42: Into the Spider’s Web Part 2
Reika ends up caught in Black Arachnid's web so Yoshi has to duel him to save both Derek and Reika!
Chapter 43: Face Your Fears
Unable to shake his fears regarding the Shadow Riders, Jaden begins having nightmares about the destruction of his friends and is suddenly challenged to a Duel by a Duel Monster Spirit named Kaibaman.
Chapter 44: Zero ATK Power!
Chazz is forced to Duel his brother Slade with the fate of Duel Academy on the line. The match stipulation states that Chazz cannot use any monsters with more than 500 ATK, so Chazz has to build a completely new Deck to even qualify for the match.
Chapter 45: Duel with an Amazon Part 1
The fifth Shadow Rider comes.
Chapter 46: Duel with an Amazon Part 2
After Bastion's defeat, Jaden goes up against Tania.
Chapter 47: Duel at Sea
Jaden duels Admiral, whom he mistakes for the next Shadow Rider.
Chapter 48: Operation: Cheer Up!
Jaden's gone so the gang does what they an to cheer Syrus up.
Chapter 49: Every Rose Has Its Thorns
Now fully recovered, Iris has to duel in order to remain in the Obelisk Dorm!
Chapter 50: Spiders on the Move
Recovered from his time as a Shadow Rider, Derek must duel to see if he stays in the Obelisk Dorm!
Chapter 51: Darkness of the Abandoned Dorm
Chapter 52: The Gladiator Assault
The sixth Shadow Makes his appearance!
Chapter 53: The Thief
A card hunter comes to Duel Academy looking for Reika. What does this Card Hunter want that Reika has? Everyone else soon learns a little bit about Reika's past with her Blue-Eyes Dark Dragon card.
Chapter 54: Discovered?!!
While looking for something to do, Reyna stumbles upon something.
Chapter 55: Syrus vs. Reyna
In order to get his spirits up, Reyna challenges Syrus to a duel.
Chapter 56: Fun in the Sun!
After Jaden returns to Duel Academy, Reyna thinks it s a good time for everyone to hang at the beach!
Chapter 57: Dark Scorpions Infiltrate
Chazz duels the seventh of the Shadow Riders, the spirit of the "Don Zaloog" card, who leads the rest of the Dark Scorpions.
Chapter 58: The Undefeated Pharaoh?
Jaden duels Abidos the Third, the eighth Shadow Rider.
Chapter 59: Alexis’ Reason
Alexis duels Titan, the ninth of the Shadow Riders, in an effort to recover the lost memories of her brother.
Chapter 60: School Festival: Duel Spirit Day
The annual school festival has arrived, and each dorm puts on a celebration.
Chapter 61: School Festival Duel: Ice Appears!
Reyna ends up dueling a girl who has a Deck of Ice Monsters.
Chapter 62 School Festival Duel: Dark Magician Girl Appears!
A girl resembling "Dark Magician Girl" appears, and ends up Dueling Jaden.
Chapter 63: Put on Ice Part I
The tenth Shadow Rider appears and duels Alexia.
Chapter 64: Put on Ice Part II
Snow Queen's defeat over Alexia makes Reyna challenge her.
Chapter 65: Zombies at Duel Academy
The eleventh Shadow Rider makes his debut.
Chapter 66: The Gambler
Someone from Alexis' past comes to Duel Academy.
Chapter 67: Shadows of the Past
Someone from Reika's past returns and the Gang learns about the Dragon Queen's past which she hasn't told anyone about.
Chapter 68: The Final Shadow Riders Appear!
Professor Banner has vanished, and a search party is organized. Meanwhile, the final Shadow Rider is on the move, and begins isolating each remaining Spirit Key holder to Duel them.
Chapter 69: Amnael’s Threat
Jaden duels against the twelfth Shadow Rider and makes a shocking discovery.
Chapter 70: The Knightmare Knight’s Challenge
The final Shadow Rider makes his move. But why does Reika have a strange feeling about him? Like she's seen him somewhere...
Chapter 71: Chazz in Love?!
Chazz steals the Spirit Keys and duels Alexis in hopes of getting a date.
Chapter 72: Sacred Beast Rising Part I
The true leader of the Shadow Riders, Kagemaru, reveals himself and challenges the Yuki Siblings, while utilizing the Sacred Beasts in an attempt to take over the world.
Chapter 73: Sacred Beast Rising Part II
Jaden, Reyna, and Hayden continue their duel with Kagemaru, and the latter Summons the third of the Sacred Beasts, "Raviel, Lord of Phantasms".
Chapter 74: Chumley's Dream Job
When Chumley gets offered a job by Maxmillion Pegasus, he has to duel Crowler to prove that he's ready for a job with a duel! Can Chumley win against Crowler?
Chapter 75: Final Match: Cyber End Dragon vs. Elemental Hero Shining Flame Wingman
It's time for the Graduation Matches and Zane and Alexandria made it to the top, so now both must chose a student to duel as their final duel. selects Jaden Yuki as his final opponent at Duel Academy while Alexandria selects Reyna. Who will win? Cyber End Dragon or Elemental Hero Shining Flare Wingman?
Chapter 76: Final Match: Cyber Cerberus vs. Elemental Hero Terra Firma
It's now time for Reyna and Alexia's duel. Who will win? The Cyber Cerberus or Elemental Hero Terra Firma?
Chapter 77: Epilogue: Foretelling Trouble
The school throws an End-of-the-School-Year Party and everyone is having fun. While having fun, the gang are trying to get Zane and Reika, who was able to bring Jasper to the party, to tel how they became an item.