Yusei was named after the Yusei particle, a particle discovered by his father, which was capable of bringing other particles together. His father hoped that he would become the bond who brought people together.
Yusei was once in a Duel gang, The Enforcers, along with Jack Atlas, Crow Hogan and Kalin Kessler. Kalin was one of his closest friends. Yusei Dueled with him once and lost. Together the Enforcers defeated all the other Duel gangs in the area, taking over all of Satellite. They were proud of their accomplishment, but lost sight of why they started the gang in the first place. Yusei and others thought that they had become shells of their former selves, but Kalin did not feel as such. He did not want to admit that their conquest was over and looked for tougher enemies. Eventually he decided to fight the entirety of Sector Security. Yusei, Crow and Jack did what they could to stop Kalin, but they failed and he was arrested. Kalin interpreted their efforts to stop him, as a betrayal and thought that they sold him out to Sector Security.
To hide from a reporter, who was staling him, Yusei hid out at the player's house, for a while. He admitted to not being good at dealing with such people. As he was the new king, they were always looking for him to do something sensational. The player blamed this on the previous king and Yusei agreed. When he thought he had hid long enough for the reporter to give up, he got ready to leave and the player offered to walk him halfway. Yusei thought that would make him stand out less and agreed.
Yusei and the player went as far as a back alley and decided Yusei would be okay form there. However as Yusei was thanking the player, he felt a pain in his Mark of the Dragon, due to the presence of Tetsu Trudge, who was possessed by the Dark Signers. He recognized Trudge from their last Duel and suspected he was there to arrest him again. He warned Trudge about what happened last time, but Trudge said he was not interested in arresting him, but wanted to get rid of him for good. Yusei asked what was going on and Trudge introduced himself as a Dark Signer, who had come from the Underworld to meet him. Yusei wondered what a Dark Signer was and Hiroshi Kumakura (Lioside) said to Duel him and Trudge, if he wanted to find out. Trudge warned Yusei that it would be a Shadow Duel and that the darkness might remind Yusei of the meaning of the mark on his arm. Yusei accepted, so he and the player faced Trudge and Hiroshi in a Tag Duel.
Yusei and the player won. Yusei thanked his partner and commented on how real the Shadow Duel felt. He tried questioning Trudge, but found that he and Hiroshi had no memory of the Duel. Trudge remembered blacking out earlier and suspected Yusei had done something to him. Trudge fell unconscious again and Yusei realized his mark was no longer throbbing. He decided to call it a day and thanked the player for his help.
Yusei learned that his fate is connected with the legend of the Crimson Dragon. The battle between the Crimson Dragon and the Wicked Gods, to decide the true ruler of the world, is repeated every 5000 years and he heard that it was almost time for that battle to start again. He learned what his Mark of the Dragon was a mark of the Crimson Dragon and the mark of a chosen Signer and that the Dark Signers are his enemies and servants of the Wicked Gods. In order to stop the world plunging inot Darkness, he needed to defeat the Dark Signers. He learned that there is more than one Dark Signer and the two members of Sector Security that they Dueled earlier were not actual Dark Signers, but were controlled by a real Dark Signer.
Yusei returned to the player's house and woke him up to tell him what he had learned. He filled him in on his plan to gather the other Signers, in order to defeat the Dark Signers. Although, the player was not a Signer, Yusei felt a strong bond between them, when they Dueled together, and thought that his assistance would be valuable.
The player and Yusei went to the hospital to meet Akiza Izinski. However Akiza had recently lost her friend, Sayer, whom she believed to be the only person in the world who truly accepted her. Jack Atlas explained that her mental anguish drove her psychic power out of control, preventing the doctors from being able to get close to her. Yusei tried to calm her down, but Akiza mistook the intention of his visit as him coming to mock her. She offered to show Yusei her power again, but told her not to bring her hate into a Duel. She reminded Yusei that he had told her that her friend would guide her and asked if it was a lie. He claimed that it was not, but she refused to believe him and accused him of wanting to take away everything dear to her. Jack warned Yusei that at this rate, her power was going to start doing serious harm. Seeing no other way about it, Yusei decided that a Duel was the only way to reach her. Akiza interpreted the challenge as them being enemies, destined to battle, but Yusei claimed it was a test of the bond of their friendship. He asked Jack for help, so Jack decided to pair up with Akiza.
During the Duel, Akiza's rage calmed down and she managed to control her power. After he and the player won, Yusei told Akiza that there are people who believe in her and need her. He explained that Sayer had only been using her and was not a real friend. He stated that he believed in her, not because he was a Signer, but because he was a Duelist and a friend. With encouragement from Yusei, Akiza agreed to help the Signers.
Kalin Kessler, now a Dark Signer, confronted Yusei and Dueled him. During the Duel, Yusei learned that he was responsible for Kalin becoming a Dark Signer. Kalin Summoned "Earthbound Immortal Ccapac Apu", which was Summoned by absorbing the souls of other people. Yusei thought that Kalin was much stronger than when he had known him before and considered himself lucky to survive the Duel.
Yusei visited the player and told him about his encounter with Kalin. He felt it was his duty to face Kalin again and that he owed Kalin, for making him become a Dark Signer. He wanted the player to witness the Duel and invited him to come along.
At the old Enerdy system, Yusei and the player met up with Trudge. They went to the area, where Yusei agreed to face Kalin again. Kalin saw the player and asked if Yusei betrayed him for the player. Yusei explained that he did not know the player back then and briefed the player in on his and Kalin's history. Kalin still believe that Yusei had chosen the player over him. Wanting to send both of them to their graves, he possessed Trudge, so he could face Yusei and the player in a Tag Duel. Yusei apologized for dragging the player into this, but said he needed his help and they accepted the Duel.
Yusei and the player won the Duel. Yusei still refused to cast a friend aside and vowed to save Kalin. He asked Kalin to join him, insisting it would be like the old days. Kalin explained that when he became a Dark Signer, he had a desire to have one final Duel under The Enforcers' name. He said that he could never truly hate Yusei and thanked him for the good times, before disappearing. Yusei wept and insisted that Kalin had always been his friend. He vowed to everything he could to defeat the Dark Signers for him.
Yusei visited the player and informed him that he planned on putting an end to the battle. He was going to the Old Enerdy system, where he was sure the Dark Signers would be waiting to fight him. He confessed that he thought he was wrong for getting the player involved in the conflict, but still did not think it was right to leave without asking the player if he wanted to help.
At the old Enerdy system, Yusei and the player met the Dark Signers Devack and Roman Goodwin. Roman said that he never thought he would Duel the son of Dr. Fudo for the 5000-year reign. Roman told Yusei about work he had done with Yusei's father and how he had discovered that the Enerdy system they had been working could be used to revive the gods. Yusei's father had disagreed and developed a device capable of shutting the Ener-D system away. Four keys were necessary to activate the device, "Ancient Fairy Dragon", "Black Rose Dragon", "Red Dragon Archfiend" and "Stardust Dragon". However Roman continued the research and activated the Ener-D system, opening a door to the Underworld. Yusei realized that the incident with Old Ener-D was not an accident. Roman claimed that the world needed to change and that he decided to make it happen. Yusei questioned his position to make that decision for everyone else and how many lives he must take to satisfy his arrogance. Roman replied that he would not expect a Singer to understand. With nothing left to say, he challenged Yusei to a Duel. Devack offered to Duel for him, but since there were two opponents, Roman suggested that they Tag Duel against Yusei and the player. Yusei vowed not to forgive Roman and to end everything now, making Roman pay for the people who lost their lives to him.
After winning the Duel, Yusei asked if Roman knew how many lives he had ruined with what he called "destiny" and if he knew the pain endured by the survivors. Roman laughed that it was not the end, as even stronger god had already been released.
Three Emperors of Iliaster
Yusei heard rumors of the Ghost Duelists, stating that the Ghosts challenge Duelists whenever they see them and inflict serious injury on their opponents. He heard that Sector Security were on the case, but were unable to identify the Ghost Duelists, as they flee quickly and vanish after their Duels. He informed the player of the rumors and the player then accompanied him, as he went shopping for Duel Runner parts.
At Combat Lane, Yusei and the player heard two men being troubled by opponents, who had just defeated them. They went over to see what happened and confronted the winners of the Duel, Fake Dean and Fake Wade. Yusei realized that they were Ghosts and accused them of corrupting the art of Dueling. He vowed to make them pay and they initiated a Tag Duel, forcing the player to take part too. After winning, Yusei demanded that the Ghosts tell him why they had been causing trouble. Wade replied that they had come to the world to eliminate unnecessary beings. Yusei did not understand what that had to do with injuring other Duelists and asked how they had the power to injure people through Dueling. Dean and Wade replied that Yusei would eventually understand if his species is on the correct evolutionary path.
After they crashed, Yusei realized that Dean and Wade had been robots. Trudge and Mina Simington then arrived to investigate the scene. Yusei explained that the Ghosts are robots and Trudge was surprised, as the robots were actually Duel Bots, which were being developed by Sector Security. Trudge explained that some had been stolen recently and Yusei wondered who would want them and for what purpose. Mina thanked Yusei and the player for their help, although Yusei thought he had not done much.
Yusei decided to ask the player to be his partner in the World Tag Duel Grand Prix (WTGP), as he had felt the potential fight Duels in a new way, the last time he Tag Dueled with the player. Yusei's partners for the WRGP, Jack and Crow Hogan, were mad and surprised, respectively, when he broke the news that he wanted the player as his partner.
The player agreed to be Yusei's partner. As practice, they faced Sherry LeBlanc and Vizor. Yusei suggested that they begin with one-on-one Duels, but Sherry thought that would be a waste of time, since the WTGP is a Tag Duel tournament. Vizor said that Yusei would need to push to his limits for the WTGP and Sherry questioned his decision to have the player as his partner. Yusei explained that the player helped him defeat the Ghosts in a Tag Duel, but Vizor insisted that the Ghosts are not nearly as good as the "real enemy", Iliaster, whom he claimed are manipulating the events behind the WTGP. Sherry wondered if Yusei was prepared to face such an opponent, with the player. Yusei replied that he and the player still had a bit of work to do before they would be ready, but felt a certain potential when they Dueled as a team before. Sherry was unconvinced and thought that Yusei should be her partner, but Yusei stood by his decision. Seeing that words would not be enough to convince Yusei, she challenged him to a Tag Duel. Vizor teamed up with Sherry to test the potential Yusei was talking about and see how he would reach a "Clear Mind".
Yusei and the player won the Duel. Sherry admitted that the two of them did share a powerful bond and allowed them to be partners. Vizor said that perfecting the Clear Mind would not be easy and that he looked forward to seeing how Yusei and the player would progress as a team. After Vizor and Sherry left, Yusei commented on how he was able to focus entirely on the Duel and nothing else. Although he was unsure what Clear Mind was, he felt he had found a clue.
When new Domino City became overrun by Ghosts, Yusei warned the player that anyone with cards was being attacked. The player mistook Yusei's visit as request to help fight the Ghosts. Yusei tried to put him off the idea at first, but the player suggested that they are a Tag Team, no matter how rough times get. Yusei agreed and said he was embarrassed that he needed to be reminded that.
Yusei and the player defeated two Ghosts on the highway. As they prepared to find more of them, they were confronted by Primo and Fake Dean. Primo told Yusei to stay out of his way and Yusei asked why he was sabotaging the tournament. Primo insisted that the tournament was meaningless and that the Ghost Duels are to determine who gets to survive. Yusei retorted that Duels are never to be forced on the unwilling. Primo replied that he would like to see Yusei stop him and challenged him to a Tag Duel. Yusei warned the player that there was no guarantee that they would come out of this Duel alive, but was surprised to hear that he was still willing to fight.
Yusei and the player won and Primo accused them of being ignorant to the fact that their evolutionary path was going in the wrong direction. He reminded Yusei of the Zero Reverse and said that the same mistake was going be made again, so he and his accomplices decided they must correct things. Yusei argued that humans do err, but they learn from their mistakes. Jakob and Lester then appeared before Yusei and introduced themselves and Primo as the Three Emperors of Iliaster. They explained that their actions were to change the future. Jakob suggested that Yusei Duel them if he wanted to know the whole story. Yusei accepted, but they explained that it was neither the time nor the place, but the time would soon come.
Jakob and Lester chose the outskirts of New Domino City, where a meteor fell, as the location for their battle. Before confronting them, Yusei told the player about the arrangements and his certainty that it was a trap. However he felt the bond they had developed would be enough to overcome the trap.
At the meteor crash site, Yusei asked Jakob and Lester why they wanted to change the future. Jakob considered Yusei worthy enough to know and explained that Iliaster is an organization in charge of correcting the world's history. He said that they travel to the past and guide humans the proper way when the choose a foolish way. However he claimed the tragic future caused by Dr. Fudo's invention of Ener-D was unavoidable, regardless of how much correction was done. Lester said that they attempted to stop it before, by destroying Ener-D, causing Yusei to realize their involvement in Zero Reverse. However that temporary destruction was not enough to erase it from history, they said, so they have come again to perform a new correction; to destroy New Domino City. Yusei refused to let them do that and insisted that they Duel.
Although Yusei and the player won, Jakob and Lester said that it was not enough to stop them. A lithograph then fell from the sky, much to Lester's surprise. Jakob said that this one belonged to Yusei and the player and Lester asked if he was saying they could hear the voice of the divine. After Jakob and Lester left, Yusei touched the lithograph, under the player's advice, causing him to acquire the card, "Shooting Star Dragon".
Yusei received an anonymous letter, not knowing at the time it was from No Money Yayoi (Rei). It stated that Kalin was in the frontier. Yayoi had been involved in illegal trading with people in the frontier and knew that this letter would send Yusei there. She hoped that as a result, Yusei would eliminate all the people she had been illegally involved with.
Yusei visited the player to invite him to the frontier, although he would not tell him where they were going. Yusei brought a poncho with him to blend in. They saw the locals, Shuji Kubota (Terence) and Enzo, say that they had had enough and were going home. They were callously stopped by Simon and KENYoU. Enraged Yusei tried to stop them, but KENYoU told him to mind his own business, as they were just bringing back workers who had ditched their job. Yusei refused to turn his back on such brutality. Simon said that he hated to solve anything with violence, so Yusei suggested that they Duel. Simon was interested and KENYoU said that if Yusei and the player lost, they would have to join Kubota and Enzo as workers. Yusei again apologized for getting the player into trouble and the two of them prepared to Duel Simon and KENYoU.
Yusei and the player won, giving Kubota and Enzo a chance to escape. Yusei advised that they get out of the area and lay low for a while. Enzo suggested that Yusei and the player come with them, as Simon and KENYoU might come back soon, but Yusei declined as he had business to attend in the town. Kubota explained that he and Enzo were guards at a mine, containing minerals, used for Duel Runner parts. However they had been forced into labor and explained that law and order were ignored in the area, in favor of money and power. They warned Yusei to be careful, as he had been marked by men, who run the town. Kubota explained that there are two apposing gangs, led by Jaime and Syun, who called the shots in the area. Enzo added that the gangs were wanted by Sector Security and had been driven out of the city, causing them to wind up in the frontier. Yusei thanked them for their information before parting ways.
This section is missing information from Yu-Gi-Oh! 5D's Tag Force 5, "poncho" Yusei's second event..
Yusei and the player Tag Duel against Jaime and Carly Carmine, after which Yusei and the player became Jaime's bodyguards.
After returning to the frontier, Yusei and the player met Jaime. Yusei noted that the townspeople seemed tense and Jaime explained that the time had come to settle a score with Syun. With a battle to determine who controls the town looming, Yusei suspected Kalin would show up. After a confrontation between Jaime and Syun, Jaime got his bodyguards, Yusei and the player to face Syun's accomplice, Kalin. Yusei said that because Kalin never turns his back on a Duel, he knew he would find him there. Kalin felt that Yusei was crazy for coming all this way for him. Yusei said that he came to take Kalin back, but Kalin claimed his life was over a long time ago and that he was better off left in the frontier to rot. Jaime interrupted their exchanges, urging them to get on with the Duel, and Syun worried that them knowing each other could become a distraction. Yusei explained that they would be Tag Dueling, but Kalin insisted that he did not work with partners. Yusei ordered him to pick a partner or the Duel would be over. Mathew volunteered to be Kalin's partner and the Duel began.
Yusei and the player won the Duel and Syun and Mathew retreated, not wanting to work in the mines. Jaime thanked Yusei for his help, but Yusei insisted that the town is not be Jaime's to control. He reminded him that the rules of the town state that whoever wins the Duel gets everything. As the winner, Yusei wanted to return the town to its people. Jaime was unhappy and said that Yusei would not get away with this. Yusei offered to Duel him to settle things, but he fled and vowed to get Yusei for that.
Kalin congratulated Yusei for winning, but Yusei reminded him that the player had won too. Kalin then realized that Yusei and the player had a bond that he and Mathew lacked. Yusei reminded Kalin that he came to save him and Kalin admitted to being saved many times by Yusei. When Yusei invited Kalin to come back with him, he refused because he wanted to repay for his sins against the town, by helping out its people.
Following what Carly said about her investigation of the town in the frontier, Yusei researched rare metal transaction records and figured out who was buying it. He figured that they were illegitimately controlling its movement on the black market and decided to check the warehouse from the transaction records. He and the player went to the junk market, where Yayoi was issuing orders to Shuji Maruyama (Gillian). Yayoi warned Yusei that he should not be barging in like that. Yusei asked if she knew Jaime and Syun and said he wanted to inquire about illegal rare metal sales. Yayoi claimed to not know what he was talking about and insisted that she was an honest merchant. Yusei requested that she drop the act and warned her that turning in the chip with her records to Sector Security would uncover everything. Yayoi maintained that she did not know what he was talking about. She asserted that she was too busy to deal with Yusei and the player and asked that Maruyama remove them. Yusei asked how long she planned on keeping up the act, but she ordered him to come back with solid evidence if he was going to make accusations. Kalin then arrived on the scene, saying that if she wanted evidence, he had it. He brought Syun with him and declared that Syun was willing to testify if necessary. Yayoi was disappointed, as she was just finished doing business with Jaime and Syun, and admitted to being the one who sent Yusei the letter. With no other options, she suggested that they settle the problem with a Duel. If she lost, she would go before Sector Security, but if she won they would pretend the problem never happened. Yusei and the player paired up to Tag Duel against Yayoi and Maruyama.
After Yusei and the player won, Yayoi was unwilling to let them take her and tried to run, but was cornered by Jack and Crow. With The Enforcers reunited Yusei asked Kalin if he was still going to return to the frontier. Kalin replied that he still had to live his life there. Yusei was sorry to hear that, but said he would be missed.
The player is able to give Yusei gifts. The following tables detail how much he likes or dislikes the gifts.
During the games, Yusei takes part in the following Duels. While it is possible for the player to achieve results different than the ones given below, the ones necessary for completion of the stories are listed.