Chapter 1: A New Threat
Upon returning to duel Academy, Jaden has a change in personality. Everyone notices it, including Kylie, who is very confused about his change. Meanwhile, the duel disks cease to function properly, and a new enemy appears.
Chapter 2: Jaden Leaving
In order to keep his friends and family safe, Jaden decides to drop out of duel Academy, however he is convinced to stay by Sartorius and Kagemaru. While talking to them, they are attacked by the same black-clad man from before, who reveals to be called Trueman, or Mr. T. Elsewhere, Atticus appears to be having nightmares and Yusuke Fujiwara continues his mysterious activity.
Chapter 3: The Truth Behind Darkness
In order to recover his lost memories about the Abandoned Dorm, Atticus duels Jaden in hopes that it triggers something. Meanwhile, Yusuke Fujiwara continues his mysterious activities.
Chapter 4: Neos vs. Divine Dragon
After recovering Atticus' memories, Yusuke Fujiwara appears but only to be the duel Spirit of Honest. He vows to avenge his master, but is ultimately talked down by Jaden. Trueman attacks again forcing Jaden to reveal a secret he has kept from his friends since returning from the Dark World.
Chapter 5: Confession
Jaden tells Kylie what happened after he went after Yubel and explains why he didn't tell her before.
Chapter 6: Duel Party Part 1
The junior students at Duel Academy organize a Tag dueling tournament, where the senior students duel against the junior students. Jaden and Kylie end up paired up. They manage to win all their duels, even though Jaden does not use Kylie's cards. Their friends mention this to Kylie, but she waves it off, saying that it's OK and besides, her traps focus around the Darklights, and can't really help Jaden anyway.
Chapter 7: Duel Party Part 2
The finals of the duel Tournament have begun and Jaden and Kylie have made it to the top. During the duel, Blair activates a card allowing them to switch partners. In the end, Kylie manages to help Jaden slowly regain his love for dueling and the two start a slow relationship.
Chapter 8: Psycho Shocker
Zane washes up on the beach around Duel Academy, somehow still alive. Syrus and Kylie are thrilled to learn the news. While Zane is recovering from his heart problems, a Psycho Style duelist named Makoto Inotsume defeats Chancellor Sheppard and wishes to duel Zane to destroy the Cyber Style once and for all. Despite his brother's and Kylie's pleading, Zane still duels Inotsume anyway.
Chapter 9: Syrus Stands Tall
Syrus takes up his brother's deck to save the Cyber Style from the Psycho Style duelist Makoto Inotsume. While training, he cannot get the Deck to function properly for him, but discovers something about Zane's heart condition in the process. Syrus ultimately combines the deck with his own to form a new one, and uses it in his confrontation with Inotsume.
Chapter 10: The Path of a Pro-duelist
Chazz aims to become a Pro League duelist, but cannot acquire a sponsor. Dr. Crowler arranges for him to become the assistant of Aster in an effort to help him become a better duelist and learn the basics of the Pro League.
Chapter 11: Armed Dragons vs. Destiny Heroes
Chazz duels Aster in a faux duel organized by Mike, a duplicitous television producer. Chazz enlists Jaden's help to even the odds, as if he wishes to defeat Aster, then he wants to do it on his own, not due to Mike's interference.
Chapter 12: Blast to the Past
With graduation approaching, Dr. Crowler begins to revert to his old ways, and Jaden duels him to find out why.
Chapter: Start of the Graduation Duels
Duel Academy's Graduation duels begins, and Jaden duels a second-year student named Taigo Sorano. Meanwhile, Trueman's attack begins in Domino City, where he begins absorbing residents into the World of Darkness. Jaden learns of the news from Axel and before heading out, asks Atticus to look after Kylie...
Chapter 13: Sartorius' Return
Once arriving to Dominio City, Jaden is saved from Trueman by Sartorius, but the latter is only part of the plot, being forced to duel Jaden in order to save his sister, Sarina.
Chapter 14: Arcana Force vs. the Heroes
Jaden's duel with Sartorius continues, with the latter intent on saving his sister, Sarina. Jaden figures out the key to bypassing Sartorius' combination of "Tour of Doom" and "Sowing of the Fool".
Chapter 15: Jaden's Illusion
After defeating Sartorius, Jaden begins to hallucinate and thinks Trueman has taken over Jesse. On the island, Trueman has taken the appearance and Deck of Taigo Sorano and is using them to defeat various students, continuing his siege, and absorbing people into the World of Darkness.
Chapter 16: Atticus' Returned Memories
Trueman's siege continues, and the entire school, save for Atticus, Reina, Kylie are absorbed into the World of Darkness. While Reina goes off to find anyone else, in an attempt to free the others, Atticus confronts Nightshroud, with Kylie watching from the sides...
Chapter 17: Red-Eyes vs. Clear World
Atticus continues his duel with Nightshroud as the latter reveals he has possessed Yusuke Fujiwara. Fujiwara's "Clear" monsters are unaffected by his "Clear World" Field Spell, and thus its devastating effects are only inflicted to Atticus.
Chapter 18: Battle Royal: Heroes and Beasts vs. Clear World
Following Atticus’ defeat to Nightshroud, Jaden and Jesse do a Battle Royal with Nightshroud. During the duel, Nightshroud attempts to turn Jesse against Jaden. Jaden vows to save Yusuke Fujiwara from Nightshroud on behalf of Honest. While they duel, Reina watches with worry.
Chapter 19: Bonds of Friendship
Jaden and Jesse continue their duel against Nightshroud to save Yusuke Fujiwara. Nightshroud uses Trap cards to manipulate the attacks and attributes of his opponent's monsters, while Jaden and Jesse narrowly avoid defeat after defeat.
Chapter 20: Jaden vs. Nightshroud
After defeating Yusuke, Jaden and Reina, try to figure out what happened to everyone. After getting a video the two head outside to meet their true enemy: the real Nightshroud. Upon reaching the outside, the Yukis discover that the Andersons have vanished, just like the others. Nightshroud reveals his true form, as well as the origins of the universe. Jaden and Nightshroud begin their final confrontation.
Chapter 21: The Final duel
Jaden attends his graduation ceremony and ends up traveling back in time, where he duels Yugi Muto when he was at his strongest - just after winning the Battle City tournament and acquiring the Egyptian God cards.