Story
The storyline of Over the Nexus does not immediately tie into that of the anime, unlike the previous two games. The player more or less keeps to their separate plot until the story reaches the halfway point, where it starts using events from the WRGP arc of the anime. As EXVC cards are not present in the card database, the plot simply ends where Aporia would have been introduced into the story.
Chapter 1 - The Beginning - The Frontier Lands, Crash Town
Main article: The Beginning: The Frontier Lands, Crash Town
The story starts in the deserted city of Crash Town. The player has a dream of becoming the best duelist, but they are awakened by Klaus, telling them that their dream won't be real and then Klaus goes to work on the mines. The player heads to Nico and West's hideout, where they duel to pass the time until the nearby card shop opens.
The card shop is hosting a Rental Deck Tournament, where participants face off using pre-made Decks. One contestant has yet to arrive and so the player fills in for them. After defeating all opponents, the player heads home, only to be stopped by Bronson, who was the tournament participant whom the player replaced. Bronson is soon defeated by the player, and remarks that the player has done well for winning in his place.
The Player goes back to his house. There, he finds Klaus, who is telling him that the next day the two must go shopping in Satellite.
Chapter 2 - The Encounter - Team Satisfaction
Main article: The Encounter: Team Satisfaction
Before the player and Klaus leave for Satellite, Toru requests that the player help him purchase some Duel Runner parts.
After their arrival in Satellite, the player and Klaus go their separate ways to get what they need. The player is soon sidetracked when he/she meets a girl named Lilie who is looking for Crow. They find him, but Crow mistakes the player as a kidnapper and duels them. Lilie soon clears the misunderstanding and leaves with Crow.
The player then continues to look for Duel Runner parts, and meets Gordon, who recommends a shop. After making the purchase, Gordon ambushes the player and steals the parts. The player gives chase, only to be stopped by gangsters along the way. However, Team Satisfaction appears and engages the gangsters, allowing for the player to pursue Gordon and retrieve the parts.
On the way out, two of the Team Satisfaction members - Yusei and Kalin - introduce themselves to the player. Yusei checks the parts purchased by the player and realizes that they simply consist of junk stuck together. While Yusei goes off to get functional parts, Kalin heads back to the Duel Runner shop to get Toru's money back. The player also wishes to thank the remaining member, Jack. On meeting Jack, the player gets into a duel for sport, and soon gets friendly matches with the other members of Team Satisfaction.
With Yusei's recommended parts in tow, the player returns to Crash Town.
Chapter 3 - The Turning Point - Just Me and My Duel Runner
Main article: The Turning Point: Just Me and My Duel Runner
Back at Crash Town, the player hands over Yusei's parts to Toru. Toru notes that they are of much better quality than what he asked for, and begins work on the Duel Runner. The player also relays the story to Nico and West, and Toru arrives at the hideout to announce the completion of his Duel Runner. They all head to the outskirts of the town, where Toru drives his Duel Runner around and even lets the player attempt a test drive.
Soon, Toru declares that he will be moving out of Crash Town and into New Domino City. Klaus forbids the player to go along, saying that they would just waste their time there.
The next day, the war between Malcolm and Ramon escalates, and Nico is nowhere to be found. The player sets out to look for her and escort her back to his home, dueling through members of the warring factions along the way. With the siblings reunited, Klaus lets them stay for the night before getting them to their home. Klaus notes that the player has been improving and challenges him to a duel to ascertain it.
Having confidence in his grandchild's ability, Klaus reveals a Duel Runner hidden in the basement of the player's home. He mentioned that the player's parents were Turbo Duelists who lost their lives in an accident, resulting in his initial reluctance to allow the player to ride a Duel Runner. Using the Duel Runner, Klaus plans to move out of Crash Town with the player, Nico and West. However, Nico and West have to stay in Crash Town since their father works at the nearby mines there.
Chapter 4 - Completion - New Friends, New Partnerships
Main article: Completion: New Friends, New Partnerships
Klaus and the player arrive in New Domino City. There, the player meets a mysterious woman named Misaki who happens to know his/her name. Misaki duels the player to test their ability, and then leads them into her garage. There, the player meets up with Toru, who proposes that the three of them form a Riding Team. However, the player's current Duel Runner is in no condition for a Turbo Duel, and Misaki recommends that they replace the vital parts - the CPU, engine, and frame.
The player is first pointed to Bootleg for leads on Duel Runner parts. There, the owner offers information if the player solves three of his five Duel Puzzles. Upon completion, the owner points the player to Blister's apartment, where the player receives the Duel Runner's CPU. Blister mentions that thrown-out parts also can be found in the underground duel arena, which is where the player finds the engine.
Upon returning to Misaki's garage, Misaki says that she found a frame in a locked-out scrapyard. The player heads there, only to find Blister and Bolt opening the gate to the scrapyard. Despite the fact that the frame is about to be thrown out with the rest of the scrap pile, Bolt is reluctant to give the frame away, and proposes a Tag Duel for the frame.
With the Duel Runner complete, Toru and the player decide to test it out the next day via a Turbo Duel. After the duel ends, Primo sees the Grand Design appearing. Lester and Jakob say he must have imagined the event, as it is not time for that yet. Back at the highway, Breo appears, infuriated at the player for using his practice course. He challenges the player to a race, and backs down when defeated. However, Toru and Misaki have pushed their Duel Runners too hard during the race and thus their machines need repairing.
Just then, Crow bumps into the player, remembering him/her from their meeting at Satellite. Crow offers to get Yusei to fix the Duel Runners. While Yusei prepares the parts for repairs, Klaus rushes in with a message of distress from Nico and West. As only the player's Duel Runner is functional, the player first sets off to Crash Town to settle the situation.
Chapter 5 - Going Home - Memories Long Past and a Hand of Hope
Main article: Going Home: Memories Long Past and a Hand of Hope
Back at Crash Town, the player finds West and Nico at their hideout. The kids' father, Sergio, is working under Malcolm, and he never come back home. The player decided to pay Malcolm a visit to ask about the kids' father. At Malcolm's house, the player duels with Seluga in order to meet Malcolm. Malcolm, having watched the duel, tests the player himself and is impressed with the player's skills. He offers the player to duel under him in exchange for information on Sergio.
The next day, the player duels against Kalin, who is working under Ramon. After defeating Kalin, Yusei rushes out from the flower shop, telling them that they must escape the town. He requested help from Barbara. However, she revealed that she is in fact working with Malcolm, and has no intention of helping them. Upon hearing that Lawton is returning from his training, Ramon leaves. Yusei, Kalin, and the player are captured and sent to work in the mine so that they will not disturb Malcolm's control over the town. While there, they meet Sergio. Yusei finds a path that leads outside, and the group decides to escape from the mine. While escaping, Sergio saves Kalin from a stray rockfall, and falls into the abyss of the mines.
The trio meets Toru and Misaki after escaping from the mine. They inform the trio that Malcolm and Radley are at war. They then return to town in an attempt to quell the warring factions and look for the kids. After defeating Malcolm and Radley, Lawton appears and seizes control of the entire town. While the player and Kalin team up to defeat him in a duel, Lawton states that his loss makes no difference to the fact that he now has the whole town under his command.
Lawton attempts to rally his lackeys, only to find that they have all been beaten by Jack and Crow. He attempts to escape, only to be cornered by Toru and Misaki. Lawton, along with the other gangsters of Crash Town, are arrested by Trudge and Mina. Peace is restored to the village, and it is renamed Satisfaction Town.
Chapter 6 - Changes - Preparing for the Tournament and a Looming Shadow
Main article: Changes: Preparing for the Tournament and a Looming Shadow
The player, Toru and Misaki decide to take part in the WRGP. After deciding on a team name, they start maintenance on their Duel Runners. They found the same tools left behind by Yusei, and ask the player to return the tools. After returning the tools at Yusei's garage, Trudge and Mina pay Yusei a visit, as well as informing them about a mysterious turbo duelist Ghost. Yusei also introduces the player to Bruno.
After returning to Toru's garage, the team decide to test run their duel runner on the highway. However, the player encounters Ghost, and is forced to duel him while witnessing the power of Meklord Emperor Wisel. After winning, Ghost leaves the highway. Toru and Misaki warn the player to be careful.
Back at the garage, Crow introduces the team to Akiza, a newly initiated Turbo Duelist. They decide to have a few Turbo Duels with each other to let Akiza get the hang of Turbo Duels and her Duel Runner. While racing, a mysterious Turbo Duelist appears and tells the player that he/she has to evolve his/her Synchro Summon in order to defeat the Meklords. The Turbo Duelist then leaves without a word.
A few days later, Klaus complains about Toru's duel runner being noisy at night. The player goes off to investigate, only to find that Toru's Duel Runner is stolen. As the player relays the information to Yusei, he/she also finds out that Jack's Duel Runner is also stolen. Trudge and Mina inform the player of a sudden recent surge of Duel Runner parts on sale in Satellite, and the player sets off to investigate this.
He/she goes to the shop that sold him/her fake parts years ago, and duels the shopkeeper for information on the Duel Runner parts. He reveals that he bought the parts from Syd. At the port, the player overhears two of Syd's henchmen, Ida and Kameno talking about selling Jack's duel runner. Upon getting discovered, Jack arrives and helps the player defeat Syd and his henchmen. Syd tries to escape, but is thwarted and taken away by Mina and Trudge. They help to send Toru's and Jack's Duel Runners back to their garage.
Several days later, at the garage, Akiza arrives, looking for opponents to spar with. Misaki, however, is busy working on a new duel runner program. Akiza mentions that Bruno can help with his skill in programming, and expresses her annoyance at how Yusei has been dedicating his time to working with Bruno. Bruno agrees to assist with the program, and Yusei goes off to apologize to Akiza. As the player leaves, he/she meets Leo and Luna who happen to be looking for Yusei. Jack also mentions that Bruno has finished the program for his team.
The next day, the team decide to test the new Start Dash program at the combat lane. However, Jack shows up and forces the player to duel with him. After defeating him, it is revealed that the opponent is actually an imposter. The real Jack shows up and decides to hunt down the culprit.
Meanwhile, the Grand Design appears, and the Three Pure Nobles start to put their plan into action.
Final Chapter - To the Future - State of the WRGP and the World
Main article: To the Future: State of the WRGP and the World
The WRGP finally begins. In the first match against Team Unicorn, Breo defeats Toru by causing him to Deck-out. Misaki defeats Breo, but is defeated by Andre. The player then duels with Andre, and eventually Jean, and win the first round. The next day, the team goes against Team Catastrophe. Toru defeats the first duelist, Hans. Hermann, the second duelist, causes Toru to crash his Duel Runner. The player take over Toru, and defeated Hermann and the last duelist, Nicolas. Nicolas, however, tries to crash the player's Duel Runner, but he ends up crashing instead due to Primo.
The next day, Yusei congratulates the team on winning the first two rounds. He informs the player that Crow is practicing on the highway, and the player goes to practice with him. While riding on the highway, the player is transported into a desert with a large stone tablet is in front of him/her. After hearing a voice, he/she is given a "Blank Card". The Emperors notice this and wonder why the player would be subject to this.
The next day, Toru and the player are training when suddenly the city is invaded by many Ghosts. Misaki, sensing this, transforms into the mysterious Turbo Duelist from before and drives off. The player is being chased by a group of Ghosts, who activates the Battle Royal mode. After escaping from the group of Ghosts, the player meets Primo, who combines with his Duel Runner and challenges the player, while the player's companions step up to take care of the remaining Ghosts. After Primo is defeated, Jakob and Lester appear to the player, Yusei and Jack, and explain their intention of changing the future by destroying New Domino City. When Jack and Yusei express their discontent with this future, Jakob tells them to continue winning in the WRGP to see if they truly can avert this fate.
Back at the garage, the group finds out that the history had been altered. A new team, Team New World, is participating in the WRGP. With Toru and Crow injured from the Diablo attack, Yusei, Jack and the player form a new Team 5D's to participate in the WRGP.
During the day of the WRGP, the team is up against Team Sherry, a team with only two members. Sherry LeBlanc, the team leader, explains that she is after Yliaster for revenge. After Yusei is defeated by Elsworth, the player takes over for him and defeats both Elsworth and Sherry. Sherry decides that her desire for revenge alone is not enough, and encourages Team 5D's to take down Yliaster.
Before the next race, the player is greeted with a heated argument between Jack and Harald. Harald mentions that his team, Team Ragnarok, are destined to defeat the Yliaster, but they refuse to work with Team 5D's due to Yusei's past. The team faces off against Team Ragnarok. Dragan manages to defeat Jack. The player, however, defeats Dragan, and eventually Brave and Harald, thus defeating Team Ragnarok. Harald, too, encourages Team 5D's to take up their cause of defeating Yliaster.
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