Yuga Ohdo dreams of changing the rigid and restrictive Dueling world with his inventions, which he calls "roads." One day, Yuga learns about a legend from Luke, his classmate from the next class over, who wants to become the Duel King. The two of them arrive at a mysterious monument and find the Hologram Man waiting for them. In order to be recognized as the "Duel King," Yuga must win within the time limit and install the new rules!

After beating the Hologram Man, Yuga was able to install the Rush Duel program. However, Luke wants to keep this a secret from the Goha Corporation, while Yuga wants everyone to enjoy fun Duels. The two decide to settle this dispute with a Rush Duel.

Goha Corporation has started taking action in order to eliminate Rush Duels. However, they don't directly target Yuga and his friends for some reason. Feeling that Goha might be leaving them at large on purpose in order to observe them, Luke decides to do some investigation on Romin, who's been acting suspiciously. Yuga suggests using a Rush Duel to get a read on Romin, but...

Gakuto has been feeling unsure about whether he should acknowledge Rush Duels as legitimate or not. One morning, as part of his daily routine, he tried to predict his fortune by drawing a card. The card he drew was his ace monster, "Fiendish Commander Yameruler". This gave him an idea...

The school's journalism club came to interview Yuga and his friends! Since Goha has been keeping an eye on the internet, perhaps he can spread Rush Duels without attracting their attention by using printed newspapers?! However, it turns out that the journalism club thinks Rush Duels are "shallow"! Trembling in anger at their insults, Luke decides to challenge them!

Rush Dueling has been spreading throughout the city thanks to the Seventh Elementary newspaper. When Yuga and his friends check the news, they find out that their favorite restaurant will be closing, so they head there in order to eat its famous ramen before it closes! However, they'll have to face Menzaburo the Gourmet Duelist in a never-before-seen Ramen Duel over the restaurant owner's last ramen!

Goha Corp has been having trouble eradicating Rush Duel. They currently have their eyes on Yuga's "secret notes." Goha has a group of six executives known as "Top of Hexagon," and now, one of them will be sent to Goha Seventh as a transfer student. Can Yuga and his friends protect Rush Dueling from the adults?!

It's a very hot day, and Yuga and his friends go to a vending machine to buy some drinks, but a giant shadow is standing in their way. Yoshio, who calls himself "the Post-Apocalyptic Duel King", has a grudge against Luke for some reason, so he challenges him to a Rush Duel! And the source of Yoshio's monstrous strength is Spaghetti Napolitan?! How will Luke fight against him?

There's a rumor that a dinosaur named "Gossie" has showed up in Goha City. This rumor excites Yuga and Luke's spirit of adventure. The two of them start searching for this dinosaur, and run into Kan Hakubutsu, a student from Goha 2nd Elementary School who thinks that Gossie is actually a Rush Duel Dinosaur. As Yuga and Luke search around the city together with Kan and his friends, they realize that Kan is looking for Gossie not just because of his interest in the dinosaur. He also has another goal in mind…

Romin gives out invites to a live of RoaRomin. On the big stage called "The Seven Dark Palaces", the Vocal Duelist of RoaRomin, Roa Kirishima, challenges Yuga to a 3-vs-3 match over the property rights of Rush Duels. Luke, taking the first step, is assaulted in a terrorizing Ghost Story Duel!

Yuga and co. were challenged to a 3-vs.-3 match, with Rush Dueling at stake. Luke won the first Duel, and Gakuto is determined to win the next one with his Neo Sogetsu Dueling Style. However, his opponent is someone he could have never expected!

Yuga's team lost the second Duel. With the ownership of Rush Dueling depending on the final match, Yuga and Roa start their Duel. As the Duel progresses, it turns out that there's a possibility that "Sevens Road Magician", which has never been used by anyone but Yuga, is an illegal card! Yuga is now in a pinch, as he would lose the moment he draws "Sevens Road"...

Yuga draws "Sevens Road Magician". But just when he thinks that he is going to lose for using an illegal card, Otes emerges from the ground! How did Yuga obtain "Sevens Road", and just who is Otes?!

Yuga and co. have won the team battle against RoaRomin. However, Luke tells Romin that he "won't talk to a traitorous undercover spy like her", and refuses to reconcile with her. Seeing that Romin is saddened by this, Yuga and co. came up with a plan to get the two of them to make up with each other using hearty home cooking!? It's explosive cooking!

According to Kaizo, the "relic" has showed up again! Following its instructions, Yuga and co. boarded the ship that also acts as a school building for Goha Fishing Elementary. As it turns out, the ship will be at sea for a month or so. Due to a misunderstanding revolving around Kaizo, Yuga also ended up entering a Duel in the middle of the sea against the ship's captain and Fisherman Duelist, Nanami Maguro!

As they chase after the fake Kaizo, Yuga and co. arrive at the A.I. Restaurant! Thanks to Luke forgetting their goal and overeating, they now have to wash the dishes. Romin then falls into a trap set by Arata Arai, the leader of the Washing Club at Goha 3rd Elementary. If she loses to him in a Rush Duel, she must continue washing dishes for free...

The one who stole Kaizo's data is Nail Saionji, a boy who oversees all of Goha's Duels and also says the enigmatic word "Providence". In order to retrieve Kaizo's data, Nail must be defeated.

The second member of Nail's team is Getta Taira, a member of RoaRomin! Getta was angry with Roa, so he left the band. Roa, who promised to Duel Getta, then shows up and begins his fateful Duel with Getta, where their shouts and drum beats will clash...! Just what will happen to their friendship?

A massage chair showed up out of nowhere in front of the Road Laboratory! As Yuga and co. were trying the chair out and having a nice massage, they were suddenly sent underground. A massage chair drone named Sebastian then emerged from the darkness, proclaiming itself as "Nail's butler and throne". Thus began the Duel between Yuga and the "King of Chairs"!

Yoshio goes underground together with Yuga and his friends. Yoshio is having trouble figuring out what his dream should be, so to discover it through a Duel, he volunteers to fight against one of Nail's minions. As it turns out, he'll be Dueling against Mimi, one of Goha's executives! Yoshio begins the Duel, unaware that his opponent is his mother, and Mimi fights against her son for his sake. What will be the ultimate outcome of Bubble Era vs Post-Apocalypse!?

Looking for the "Haven" where Nail is, Yuga & co. wander underground. Exhausted and hungry, they all smell a pleasant scent at the same time... before them they find a very flashy ramen shop crowded with Goha employees, "Space House". Serving an extremely delicious ramen is an alien called "Sorako"!? Where ramen is involved, Menzaburo appears! It's a Ramen Duel again!

Yuga and co. use the coupons they got from Mimi and enjoy a meal at the A.I. Restaurant. There, they feel that someone is watching them... and it turns out to be Arata Arai! After bringing Luke to the dishwashing room, Arai begins a Cheat Duel against him. For some reason, Luke can't use his special power "Luke Devil"...!?

Yuga and co. reach the Gate of Providence, the entrance to the Haven. Beyond the road lined with shops selling various kinds of providences is their destination... they open the heavy door, where the final showdown with Nail awaits. Then, a monster that transcends imagination is Summoned in a blinding light!!

Yuga doesn't show up when promised. Worried, Luke, Gakuto, and Romin go search for a way to beat Nail. They go where it all began, the Relic, and demand an answer from Otes. To give them the hint they want, Otes places a condition. That is to "win" a Duel, and to have "resolve"!

Yuga and Nail battle again. Facing the overwhelming might of "Yggdrago the Heavenly Emperor Dragon Tree‎‎‎‎", Yuga's draw carries Luke's, Gakuto's, and Romin's feelings, and is also empowered by Kaizo. Their dreams, courage, and friendship call forth a miracle.