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Jaden finally succeeds in saving the world from the Darkness, and now Graduation time has come for Jaden, Syrus and the others. However, Winged Kuriboh has something to show Jaden.
Jaden takes on the Darkness full force and fuses with Neos and Yubel in order to finally rid the world of Darkness' influence.
A mysterious person who beat Sheppard in a duel wants to beat his successor, which happens to be Zane.
Axel discovers that the disturbance was a man named Mr. T. The two of them begin a duel, but Mr. T. begins to make Axel see things.
Sartorius has Jaden on edge, but he manages to come back. He then tries to convince Sartorius to stop the duel and help him save Sarina.
Jaden arrives in Domino to look for Axel, but numerous Mr. T's begin to surround him. However, out of the blue Sartorius shows up to help Jaden. When they are alone, Sartorius then challenges Jaden to a duel.
It is time for the Graduation Duel and Jaden's opponent is finally chosen: a second year Obelisk Blue. In just one turn the student summons a level 8 monster, putting Jaden on edge. Meanwhile Axel runs into some trouble in Domino.
As the finals of the pairs tournament arrive, Jaden and Alexis are up against Hassleberry and Blair. However, Alexis and Jaden don't seem to be on the same page in their strategies.
Judai also makes the grave decision and submits his "Notification of Withdrawl" to Chancellor Sheppard. Jaden meets some people who are Sheppard's indication not to accept his Notification of Withdrawl. They are Kagemaru and Sartorius. Sartorius has come to tell Jaden that Kagemaru has sensed a crisis that might happen somewhere down the road. Then, a man in a suit appears before the three.moreless
Jaden and Jesse team up to face off against Fugiwara.
Axel has saved Atticus from Yusuke. Axel has accepted a new mission and returns to Duel Academy. Then, Jaden duels with Atticus to solve the mystery behind Nightshroud. Atticus, drawing on the power of Nightshroud, summons Red-Eyes Darkness Dragon.
Chazz's mistake causes Aster to retire from the Pro League, and he finally gets his taste of the spotlight.
After a month, Jaden has finally returned to Duel Academy, but stays inside his room. Jesse, Axel, Jim, and Adrian have all returned to their schools, and Syrus, Chazz, and Blair are all in Obelisk Blue. Then something mysterious happens to the Duel System so Chazz, Alexis, and a new student go to investigate.moreless
As the three way duel continues, Fugiwara tries to use the darkness within Jesse's heart to destroy the bond between him and Jaden.
Jaden and the others have finished their graduation album. When Crowler previews it, it causes him to act strange and force the students to do weird things. Jaden challenges him to a duel.
Mr T. has taken control of students bodies and is using them to trap students in a world of darkness, causing everyone to forget about them.
The identity of the Darkness is finally revealed. Angered by recent events, Atticus decides to duel it.
Jaden tries to return to Duel Academy, but Mr T. blocks his way. Seeing no other way out, the two begin to duel. Jaden then finds out that Mr T. uses a Crystal beast deck, which only Jesse should be using!
Chazz wants to be a pro duelist without his brothers influence. However, no one is accepting him. Crowler tells him he has a teacher for Chazz, who just happens to be Aster.
Yusuke's true identity is revealed as the card spirit, Honest. Jaden uses the power of Yubel within his soul to hold Honest's attacks back. He asks Honest about the worldwide disaster happening at the moment, and Honest begins to talk. Truman and Mr. T, emissaries of Darkness who have been waiting and seeing how things played out, come launching an attack in attempts to kill Jaden and the others! Then, Honest summons Five Headed Dragon!moreless
Hassleberry organizes a Dueling Party where everyone needs a partner. While Alexis is worrying about what her next career path will be, she winds up being Jaden's partner.
Syrus decides that he must duel Izume in Zane's place, but his practice with Zane's deck doesn't go well.
Winged Kuriboh has lead to Jaden to the King of Games, and his original owner, Yugi Moto himself! Yugi challenges Jaden to one final duel.
Fugiwara is finally defeated, but darkness still encases the world. The real darkness then confronts Jaden.