The Player has a number of customization options, including hairstyle, hair color, skin tone, clothing, clothing color, and main Attribute. However, the Player is always male.
In the beginning of the game, the Player is in the park, where Shuji and Akira accuse him of making fun of how they battle. When the Player denies it, Shuji challenges him to a battle. The player is frightened as he doesn't know how to brawl. Suddenly, Dan Kuso appears and offers to teach the player how to battle. After the Player beats Shuji, the latter tells the former that he (Player) should wait until the tournament for Shuji's real strength to be unleashed. As they run away, Shuji tells Akira he let the Player win.
Dan comments on how great the match was, and tells the Player that if he gets stronger, he could even participate in the tournament Shuji mentioned earlier. However, without a Bakugan of his own, the Player wonders how he can ever find anything like Drago. Suddenly, there is a strange flash, and a Bakugan appears, who calls himself Leonidas. He agrees to be the Player's Bakugan partner, and the Player registers for the Neo Challengers Tournament.
After he wins, he meets up with Dan, Runo, and Marucho. Dan is impressed that the player and Leonidas won their first tournament. Runo and Marucho, on the other hand, find Leonidas' aggressive attacks to be a little strange and connected to his time of arrival on Earth. Runo mentions that Tigrerra found something weird about his personality, which the player dismisses as envy, and attempts to suggest the player in finding another Bakugan partner. After they leave, Dan tells the player not to worry about them, and that the next tournament is the Supreme Tag Team Tournament. As they wait in the registration room, Dan tells the player that they are one step ahead to the UBT, the Ultimate Battle Tournament. After the Tag Team Tournament, the next one is a Battle Royale; Dan invites the player to practice together at the park.
When he exits the park, however, he receives a message saying Dan was defeated by a mysterious brawler. As the player registers for the Brave Battlers Tournament, Julie confronts him and accuses him of being that mysterious brawler. While he denies it, Julie believes otherwise, citing Leonidas' aggressiveness as proof. Runo and Marucho agree with Julie, with Runo saying that every Bakugan she's asked, even Tigrerra, haven't even heard of him, but the Player places his trust in Leonidas, shocking the Bakugan. Julie refuses to relent, however, telling him "Your name is mud in this tournament, kid."
After he wins the tournament, the player hears a strange voice say that the battle was a joke. The owner of that voice appears before the Player and reveals himself to be Marduk, the greatest Bakugan battler in the world and introduces his Guardian Bakugan: Vladitor. Runo comments on Marduk being a 'big meanie' while Marucho is surprised by Vladitor's power level. Suddenly, Dan appears, saying that he and Marduk have some 'unfinished business' for what the latter and Vladitor did to Drago. Vladitor points out that while Drago is no match for him, he is interested in Leonidas as he is different from all the other Bakugan and that there is darkness inside of him. The player isn't buying this and challenges Marduk to a battle. After the player and Leonidas won, Vladitor says that he knows what makes Leonidas different from all the other Bakugan: Leonidas was born in the Doom Dimension and that Vladitor immediately sensed the connection since he used to be a prisoner there for a long time. He then offers Leonidas to join him since he thought they are the same, but the player intervenes, saying that Leonidas is nothing like Vladitor. Not phased by this, Vladitor tells Leonidas to think about this. As soon as Marduk and Vladitor left, the player asks Leonidas if he is lying, but Leonidas confirms Vladitor's statements and admits that he originally wanted to take his anger out on other Bakugan because he felt insecure about his origins until he met the player.
After that, the player meets Shun during registration for the Maximum Battle Tournament. Just like Runo, Marucho, and Julie, Shun is against Leonidas and says that he is in the tournament to stop him from joining Vladitor, to which the player contradicts. But after losing to the player, Shun reconsiders his words and thinks that the player and Leonidas are perfect for each other. Just then, Masquerade appears, mocking Shun for his recent loss and being curious about the player and Leonidas. As the player and Masquerade battle, Masquerade is impressed by their skills and finally sees why Vladitor wants Leonidas to join his side. He even says to Leonidas that the offer to join them still stands, but Leonidas immediately refuses.
Later, while registering for the Bakugan Master Cup Tournament, Dan and the player are excited about this, with the former complimenting the player for his knowledge about the Battle Brawlers as well as skills on the battlefield. The player says that he has been following them on the Internet forever and that they are the real heroes. Suddenly, Dan comes up with an idea: if the player beats him in the tournament, he will make him an official Battle Brawler, which made the player eagerly accept. Of course, after losing to the player, Dan remains true to their deal and makes the player a Battle Brawler, thus making them teammates. Suddenly, Marduk and Masquerade appear, planning to take them down with all the other Battle Brawlers in the Ultimate Battle Tournament.
With the Battle Brawlers meeting at the stadium's registration room, they learn more about Marduk's and Vladitor's origins (the former being a Bakugan player who used dirty tactics in battle and was betrayed by his former friend, which led to his Bakugan being sent to the Doom Dimension and him holding a big grudge against all things Bakugan-related, the latter being an evil Bakugan who was banished to the Doom Dimension and later escaped after Naga stole the Silent Core). Dan then summarizes that both of them have one common thing that they want: payback. The player disagrees, saying that there is more to them. He thinks that even though Marduk has declared war on all Bakugan, he still loves Bakugan deep down and that was a partial reason why he wanted to battle in the tournament. Runo assures that Leonidas can beat Vladitor again if he beat him before, to which Shun agrees but adds that this assumes that they will trust Leonidas. Drago claims that he trusts Leonidas, regardless of his origins. With that in mind, this was enough for them to work as a team to stop Marduk and Vladitor.
Later, the Brawlers have finally prepared themselves for the Ultimate Battle Tournament, as well as showing that their Guardian Bakugan have finally evolved. As the player and Leonidas work their way through the tournament, so did Marduk and Vladitor. They take Dan and the rest of the Brawlers down as they were deemed too powerful. With only the player and Leonidas left, the Battle Brawlers give them support to win the final match in the UBT.
Once the player and Leonidas defeat Marduk and Vladitor and win the tournament, Vladitor couldn't help but feel humiliated for his and Marduk's loss. Hal-G then appears, telling them that their deal is off. However, not willing to be beaten again, Vladitor snatches the Silent Orb, which he uses to become Battle Ax Vladitor. With this new power, he filled the UBT arena with Doom Dimension hyperspace, causing the Battle Brawlers' Guardian Bakugan (except for Leonidas) to feel weakened. In order to defeat Marduk and Vladitor again, the player tells the Brawlers and their Bakugan to focus all of their strength on Leonidas, which leads to him evolving to Omega Leonidas.
With Leonidas and the player victorious, Vladitor started to fade out of existence. Marduk refused to let his partner go and was greatly saddened when the Bakugan faded. The same began happening to Leonidas. Marduk began crying after the loss of Vladitor, as he feels that the Bakugan is the only friend he can trust. The player tells Marduk to stop crying and face his loss like a man, and that the next time they battled, it would be a great battle between the two of them. The player then thanks the Battle Brawlers for their help and support. Runo then asks him if he's sad about Leonidas disappearing. He says that he is sad, but he has the feeling that his Bakugan knew what he had to do and that he is proud that Leonidas is his partner, for a while at least.
The next day, the player returns to the park as this is where he and Leonidas met for the first time. Another flash appeared and, to his surprise, Leonidas reappeared in his hands. The player asks him what happened. Leonidas replies that he doesn't know what happened either but remembers Vladitor giving him his remaining energy since he felt that Leonidas deserved it. With Leonidas back, he and the player make a promise to stay together. In the end, the player and Leonidas shout "Bakugan, brawl!", with the former throwing the latter into the air.
- According to the Bakugan Battle Brawlers video game factsheet, the Player's name was originally going to be Rikku. He was also originally intended to be a Haos Brawler.