So far, the main points of the story is following three duelists with different dreams. Shuho Kazeyama dreams of being a World Class Riding Duelist. Brought up in the Satellite after an incident, he's picked up discarded Duel Monsters cards in Satellite and used them to make a Light and Darkness Deck. Zeiya Hisaki has lived in Satellite most of her life and hates it. She's dedicated years of her life into stealing and obtaining her Dueling Deck, D-Wheel parts, and knowledge on how to use them. All of this was done in the hope of escaping Satellite. Kai Blackdragoon is a mysterious duelist who seems to only want to have fun, enjoyable duels. He hates to see suffering and fowl play and dreams to use his dueling to make people happier.
Within Satellite, Zeiya was found stealing D-Wheel parts from someone, and was met by Shuho who dueled her. Afterwards, she met Yusei and was able to finish the D-Wheel she'd dreamed of. Kai was asked by the ones she stole from to get back the missing parts. He attempted to do this, but inevitably gave up upon seeing that Zeiya was actually an honorable duelist. He gave her a powerful card, Blue Eyes White Dragon, which he obtained through mysterious means, and challenged her to a duel.
During this time, Shuho was exploring the B.A.D. Area of Satellite, where he met Seiki, a Duel Disk mechanic with few loyalties. Shuho took it upon himself to try to clean up the B.A.D. Area from the dueling gangs, but this was haulted by Sector Security trying to aprehend him. Apparently, Zeiya and Kai were captured just after a duel and sent to the Holding Facility, leaving Satellite unprotected and Shuho needing a way out. He was able to find himself a discarded D-Wheel, using it to try to escape the Satellite. As he did, he was confronted and dueled by a Security Officer named Kazu, who nearly defeated Shuho until his D-Wheel malfunctioned and he was sent into the river.
Inside the Holding Facility, Kai and Zeriya met up with Yusei, who'd been captured after going to Neo Domino and confronting an old friend who stole many important things from him. The Warden of the Facility challenged Zeiya to a duel, which she accepted despite not having her deck. Until that point, she was in despair at losing eerything she'd spent so much time gaining, but the female prisoners helped her, claiming the Warden abused them. With a deck and newfound determination, Zeiya challenged and defeated the Warden with her Blue Eyes White Dragon.
After the duel, a new man named Rex Godwin appeared, promptly firing the disrespectful Warden. As per their agreement, Zeiya was allowed to leave with Yusei, but Kai was forced to battle a Security Officer to win his own freedom. Kai managed to win, and Zeiya's D-Wheel was returned to her, meaning she could move through Neo Domino City with no other problems.
After fixing his D-Wheel, Shuho managed to get into Neo Domino, using the method he'd seenn Yusei emplore once before. Riding through the broken streets of the rejected sector of the city, he met up with Zeiya. After catching up, they were interrupted by a strange man named Jaeger who gave them an invitation to a special Dueling Tournament. With the invitation was a picture of their friends, Seiki and Yusei's friend who they had also met. This meant that they were in danger and were being used as motivation to be sure that Zeiya and Shuho entered the tournament and did their best.
Zeiya found a man named Kariya Marco, looking for practice before the tournament. They dueled, and he proved himself to be a powerful opponent. In the end, Zeiya was only able to win through the power of Blue Eyes White Dragon. Kariya took great interest in Blue Eyes White Dragon, calling it a Spirit Monster. The ending result of the duel caused Zeiya to lose confidence in her Blue Eyes, one week away from the tournament.
A day before the tournament, Zeiya and Shuho were infromed that they needed to pass preliminary duels before qualifing for the tournament, the Fortune Cup. They met with Kai, who was also in thr tournament and had to qualify. Kai, not having a D-Wheel, qualified through a duel while Zeiya and Shuho managed to win their spots through a D-Wheel race. Afterwards, they all were forced into dueling to gain their final spots. Kai dueled someone named Ruka, who was later revieled to be her twin brother Rua. Zeiya dueled the Officer Ushio, who she'd dueled once before, in a Riding Duel. Shuho dueled against Kazu, a rematch from the Satellite, with Shuho now having a very modified version of his deck. The three were able to win and saw a final duel between a mysterious and powerful Aki Izayoi and Seiki. Surprisingly enough, Aki won a hard fought duel and Seiki was sent to the Holding Facility, only able to be freed if Shuho or Zeiya could win the tournament.
The day of the tournament, Everyone was prepared for their battles, and the battles themselves were very surprising. Kai was only narrowly able to defeat Aki Izayoi in a dragon showdown between her powerful Black Rose Dragon and his Red Eyes Dragons, his most powerful and trusted cards. Kai was hurt in the duel, seeing Aki's pain and wanting to do something about it. In the end, he felt as though he failed her. Shuho battled a powerful opponent who concieded when Shuho used his ace monster, Light and Darkness Dragon. Kariya Marco, the duelist from before, defeated a very powerful dragon duelist using his Dragunity combinations. Finally, a long and hard fought duel between Zeiya and Yusei led to Zeiya's victory over his Stardust Dragon.
The next round involved Shuho and Kai, a very hard fought battle which led to Light and Darkness Dragon clashing with Red Eyes Darkness Metal Dragon. In the end, Shuho was able to win with Light End Dragon, which caused Yusei and the Duel King to become very interested in him. Zeiya was feeling ill from the night before, not sleeping as she tried to prepare for Kariya throughout the night and had no sleep. Yusei convinced her to rest before the battle as well as to trust her Blue Eyes White Dragon as she hadn't used it since the first duel with Kariya Marco. When she awoke, she was ready to duel, but Kariya already had her strategies in his mind. He used powerful carrd combinations specifically to stop her normal strategies, which forced Zeiya to use the Blue Eyes to win her duel. After the duel, however, she collapsed and crashed.
As all this happened, Shuho was confronted by Jack Atlus and challenged to a duel. Jack Atlus sent a flurry of power and combinations at Shuho, who was still able to fight back. With Zeiya incapasitated, Rex Godwin declared that the Jack/Shuho duel would be the final duel of the Fortune Cup. Shuho was about to use his Light End Dragon, Dark End Dragon, and Light and Darkness Dragon to actually win the duel, making him the new Duel King.
As this happened, Seiki was in the Facility, watching the duels with Ushio with distain. Upon seeing Zeiya crash, she forced Trudge to release her so they could go tend to her friend. The Officer relunctently agreed and they were off, after Seiki was able to fix his D-Wheel.
Within the Stadium, Zeiya was in the Medical Ward recovering. As she was, two men in robes walked into the room, looking to take her. Kai attempted to stop them, but they used a strange power similar to what he'd faced against Aki and brought him down. Shuho ran in from the noise to find Zeiya gone and Kai injured. Now Zeiya is in the hands of Divine and the Arcadia Movement, and how the story continues......