The battle begins when the story of how the game of bakugan was created with the help of Dan Kuso and many other children, and how it quickly became popular around the world. Dan faces a young boy, Akira's older brother, Shuji, as Drago and a mysterious white dragon known as Naga fight in Vestroia, with the dragon destroying itself by getting to close to the two cores - Silent and Infinity -of Vestroia. Dan quickly beats his opponent, but in a rematch, things are far more heated.

Dan goes to school and attempts to show that Drago can talk, but only ends up getting in trouble. Drago tries to get away in the panic, but gets caught by the teacher. When Dan gets back, he is told by Runo that she lost a battle to Masquerade and lost her Bakugan because he took them.

Masquerade shows up and gives the Doom card to a mysterious brawler, as Dan trains with Drago to fight him again, although Drago and Dan continue to argue and fight. Marucho speculates that the fight he had before was a draw, with the field self-destructing because of Drago's ability. They start to get along as Runo finds Tigrera, another talking Bakugan. Dan then fights the mysterious brawler named Rikimaru. Dan barely beats him

A strange talking Bakugan jumps on a bird in the beginning of the episode as Dan and Runo talk to the others about some odd construction going on in town. It turns out that this place is Marucho's house, and he's finally moved into Dan's town. After Julie gets jealous that she was not invited to Marucho's home, Runo claims she forgot. Dan takes this opportunity to tease her and call her a scatterbrain.

The battle continues with Marucho barely managing to win with the pop idols element combination working against him. Just as things look bad for Drago, Preyus once again manages to help with his element change ability, winning the battle.

Muu and her friends Takahshi and Kasuki wait at the airport for her little brother Lakoto whom hasn't come home in a very long time, then Masquerade comes and gives the boys Doom cards. Alice comes to be with the group, arriving from Moscow by plane. She feels apprehensive about telling them her visions involving her grandfather Micheal, but just as they really get to know each other they get challenged by the two brothers.

Episode starts out with Dan battling one of Masquerade's minions. He wins but then passes out. When Dan wakes up, Marucho proposes that they need all 6 attributes. He then says they should get Shun, No.1 bakugan player in the world, on their team, because he has Ventus Bakugan. Runo agrees but Dan is against it. However, Runo and Marucho go to see Shun anyway. They enter his home, only to run into traps and eventually Shun's ex-ninja grandfather. Shun's grandfather attempts to attack them but Runo and Marucho accidentally pull out their Battle Cards and stop time. They walk past him and restart time making him fall into his own trap. Runo and Marucho then hear Shun playing on his Leaf Whisle and find him.

Alice is working in Runo's Family's Restaurant, and all of the guys seem to have a thing for her. Alice is worried about telling Runo about her grandfather being Hal-G, the human who corrupted Naga's mind. Runo is still troubled about losing to Shun, and breaks a cup when Alice comes in, making Alice unable to tell her about her grandfather. Skyress asks Shun if he's all right, to which he responds, "I don't know". Dan is looking up his ranking, now at 97, and is shocked to see that Runo is nearby as well. He then sees that Shun is in 6th place, and shows that he is unsatisfied. Drago asks about Shun, and Dan tells him that he was at the Top, but then stopped playing Bakugan. Dan then tells Drago how he and Shun used to be best friends when they were young. He says that he and Shun were the ones who started the game of Bakugan, and that Shun started to come onto the chat site less and less. Shun then has a flashback about him sitting by his ill mother at the hospital, and she asks him to go get her purse. She says that there is something inside of it for him, but he says he doesn't need anything, all he wants is for her to get better. While Shun is walking to his house he wishes that she would stop worrying over him and look after herself. He gets home and sees that his grandfather left him a message stating that "things are gonna change under my house rules."

Alice finally reveals to the other Brawlers that her grandfather Micheal is the one that Naga encountered in Vestroia. When the other Brawlers learn of this they all decide to take a road trip to her grandfather's lab in Moscow to see if they can find learn anything else. When all the Brawlers, minus Julie, get there they find a video recording from Dr. Micheal that explains how bakugan entered the human world and how he was involved in that. Meanwhile all the top brawlers from around the world are invited to a party including the #2 battler Klaus Von Herzon, #3 battler Chan Lee, #4 battler Julio Santana, #5 battler Komba O'Charlie, and #10 battler Billy Gilbert.

The brawlers have settled down to eat dinner but no one except Dan seems to have an appetite as they are concerned about Julie who returned home depressed after the battle. The next day the brawlers are searching for another entrance to Vestroia without any luck. Dan suggests they go visit Julie but Alice says she probably needs to be alone right now, before the discussion can continue Shun contacts Dan saying that he has discovered another region with physical similarities as Bakugan Valley suggesting they go there to look for a door to Vestroia. Dan and the others agree to this plan and cut off communication. While Shun and Skyress wait, Skyress looks at the two maps Shun has on the computer and comments how the two valley's look nothing alike, asking herself what Shun is up to. When the brawlers return to the plane they are greeted by Julie, who has perked up and decided to move on from being depressed. With Julie joining them the brawlers take off for the other valley. While on their way there the brawlers comment on how Masquerade and his team keep showing up wherever they go and Shun states that someone must be spying for him. When Dan accuses Shun of saying that one of the brawlers is the spy, Shun denies that by saying there is one other person who knows the brawlers every move, that person being Webmaster Joe. The brawlers consider this a possibility and Skyress states that this must be the reason why Shun lied about the valley that they were heading to. The brawlers realize that if Masquerade's team is at the valley then Webmaster Joe is most likely involved with him. Once they arrive they're greeted by Chan Lee and a battle between her and Dan begins. Dan and Drago test their luck as they take out two of Chan's bakugan only for the tides to turn when Chan revives them and Dan is left with only Drago. Things go from bad to worse as Chan's bakugan has a much stronger power-level than Drago just as Chan goes in for the killing blow, Drago turns around and takes Chan's bakugan out with both Dan and Chan learning that Drago's power level increased without Dan using an ability card.

Everything begins with Klaus looking up Preyas's data saying how he doesn't possess a bakugan like him and how he would like to add it to his seemingly extensive Bakugan collection. It then switches to the brawlers as they return to Marucho's plane as another day of searching for the infinity core and a door to Vestroia ends in failure. Marucho and Preyas cheer everyone up by making takoyaki to eat.

After losing Preyas to Klaus, Marucho, who is grief-stricken, begs Klaus to return him but Klaus refuses. Klaus opens a portal to Masquerade's evil lair which Marucho and Runo both jump through after Klaus. When there they access Masquerade's computer and learn about the wonders of Bakugan evolution and its intense power. Just when they thought it couldn't get any stranger: Julio Santana! The 4th ranked brawler shows up and challenges them to a battle. Surprisingly, Dan opens his Gate Card at the same time as Runo, Marucho and Julio and is dragged into the battle. Julio insists they both take him and his Haos Tentaclear on.

The episode starts with Marucho and Preyas playing together on the beach when Preyas suddenly disappears. Marucho wakes up to find out that that was all a dream and Preyas is still gone. At breakfast Dan and Runo get in another fight that causes a rift in the brawlers. Julie wants to free Billy from Masquerade's control while Runo wants to help Marucho. Dan and Julie leave to go searching for Billy with Julie coming up with an idea for how to find him.

The episode starts with the brawlers realizing that Naga has not yet reached the level of Ultimate Evolution as he is still trapped within the Silent Core. Billy also tells them that Masquerade had shown him, Klaus, Chan, Julio, and Komba Naga who used the negative energy to brainwash them. Shun remains quiet throughout this and later leaves the team as he feels none of them will be able to beat Masquerade — Dan and Runo always quarrel, Marucho moans over the loss of Preyas.

The Bakugan Team bring Komba back home to Kenya, and soon after Marucho, Dan and Runo are challenged to a Bakugan Brawl against Klaus, Chan, and Julio. Shun, Alice and Julie are worried that they won't win as they are not working together as a team. Once on the battlefield Marucho says he wants to battle Klaus as revenge, but instead Runo battles Klaus, and he reveals his "new" Bakugan- Preyas, they win and Runo loses her bakugan.

Preyas is back and is better than ever! With Preyas on their side of the battle things are looking up for the battle brawlers. Dan, Runo, and Marucho are able to take down the remainder of Klaus, Chan and Julio's bakugan until only Sirenoid, Foretress and Tentaclear remain. Things take a turn for the worse however when Chan uses the quartet battle gate card to force Drago to take on all three bakugan at once. With help from Runo and Tigrerra, and Marucho and Preyas, and Dan Drago causes cracks in the field that release lava that encircles Drago and transforms into a meteor.

The team go to a city where Webmaster Joe is staying in a hospital. They enter the hospital and ask the receptionist where Webmaster Joe's room is and she tells them 'Room 501'. Then Dan goes looking for him, losing the others but can't find the room Joe is in and ends up the others decide to go and see Joe on their own. Runo knocks on the door and a lady says 'Come in' and they do. She introduces herself as Joe's Mother while talking about him and bringing out freshly baked cookies. Julie tries one and has some more as she loves them so much.

It starts with a young boy who is losing a bakugan battle to a teenager, then it switches to Dan's parents wondering where Dan is and when he will be home. Just as their conversation stops the ground begins to shake and when they go outside they see Marucho's plane with Dan yelling 'I'm home!' Dan and Drago relax in the bath tub and discuss the events that have happened and what they need to do next. Meanwhile Julie decides to stay at Marucho's and Shun has returned home to meditate. Runo is working in her parents' cafe while Alice is out buying groceries.

The brawlers are trying to find people to take them on in battle but no one wants to. Marucho and Julie return to Marucho's home while Dan visits Runo and Alice. While Runo isn't around Alice tells Dan that she thinks Runo is suspicious of her and has been watching everything she does. When Dan talks to Runo about it Runo admits that she is suspicious of Alice because she doesn't have a partner bakugan and she doesn't battle so why is she on the team. Runo thinks she may be working for Masquerade but Dan doesn't think so. Meanwhile Julie tells Marucho that she thinks Shun works for Masquerade because she saw Shun earlier. While Marucho searches their website for answers Julie goes searching for Shun.

The episode begins with the flashes of light indicating that a battle has just ended and Julio falls to the ground completely after he lost Tentaclear to the Doom Dimension beaten up from his battle against Masquerade who is seen walking away. Then it shows Runo who is worrying about the small amount of bakugan she has left. It then switches over to Chan who engages Masquerade in a battle, the battle ends badly however as Chan loses and Foretress is sent to the Doom Dimension. It switches back to Runo's cafe where Runo has just finished telling the brawlers that she isn't going to battle ever again with Tigrerra asking her later on if that is a good idea.

The brawlers learn that Masquerade has sent the Bakugan of his former teammates to the Doom Dimension and that Hydranoid has evolved to Dual Hydranoid. Masquerade and Dan have another brawl again. Everything is going well for Dan but just when Dan is about to win the battle Masquerade pulls out one last ability card and turns the tide.

The episode starts with six voices talking about how Vestroia is collapsing and how they sacrificed everything to save Vestroia in the past, and how now they need to find new warriors to save Vestroia. It is the morning after Dan and Drago were sent to the Doom Dimension and all of the Brawlers are taking it hard. In the Doom Dimension Drago is greeted by Reaper saying that now that Drago is there he will never get out, and Dan reunites with Drago. Meanwhile Dan's mom realizes that somethings up when the Brawlers lie to her saying that Dan went away to help a friend, and goes to Runo's family cafe to ask her about it. When Dan's mom confronts Runo about Dan's sudden departure and about how she caught Dan talking to his Bakugan one day Runo runs off saying she cannot tell her anything, leaving Dan's mother very worried. At the same time Shun receives a challenge letter from Masquerade and he and Skyress come up with a plan to find Dan and Drago.

The brawlers reunite with Dan and Drago and as they are wondering how to get back home from the Doom Dimension the six bakugan who were watching the brawlers appeared. The six bakugan introduce themselves as Pyrus Apollonir, Haos Lars Lion, Aquos Frasch, Subterra Clayf, Ventus Oberus and Darkus Exceedra. Drago recognizes them as the six ancient warriors who saved Vestroia in the past. When the brawlers demand to know what the ancients what they explain that they are searching for new warriors to save Vestroia from total destruction. The ancients say that they want Dan and the brawlers to become the new warriors and that if they do the ancients will help them escape from the Doom Dimension. But there is a condition, the brawlers must face the ancient warrior of their attribute in battle...and win or else they will remain in the Doom Dimension forever. The brawlers agree but Dan adds to the stakes saying that if they win all of the bakugan trapped in the Doom Dimension will be freed. The ancients agree then in a flash of light they separate the brawlers sending them in different directions with julie and Gorem being the first to be tested. When Julie wakes up she finds herself in her house with her sister Daisy and Tom, who is really Clayf. The battle begins with Julie facing off against Daisy, who has Clayf.

The episode starts with Marucho getting sent somewhere for his test. Marucho walks around searching for the others but has no luck in finding them just then Marucho hears a voice. The voice asks him to move and Marucho looks down to see he is standing on a frog person. This strange being asks Marucho and Preyas to get him some water after Marucho and Preyas give him the water they learn that he is Frasch the ancient aquos soldier. Frosch transforms the surrounding area into water and starts the battle using an imitation of Marucho as his partner. As the battle goes on Marucho realizes that the Marucho he is facing is his past self, from the time when he did everything his parents asked of him.

Shun and Skyress finds themselves in a town. As they look around they notice that there is no one else is there and Skyress comments that it looks like a ghost town. Just then Shun and Skyress meet a small girl who is looking for someone to play with. When Shun asks what she wants to play she says tag and makes Shun it. Shun and Skyress play with her and when they win the girl starts another game, kick the can. After that the girl brings them to the hill and shows them the sun which makes Shun and Skyress realize that it hasn't moved since they got there. Just then Shun has a flashback from when he was little about his late mother. The little girl then talks about how alone she was before Shun came and tells Shun she has one more game to play with him, bakugan.

The Battle Brawlers are dispersed into separate worlds created by the Six Legendary Soldiers of Vestroia. Julie, Marucho and Shun pass their test. Now it is time for Runo to pass her test. The Haos Legendary Soldier, Lars Lion, creates a mystical woodland area. Tigrerra and Runo find themselves wondering in a forest full of mist. Runo pleads and wishes that Dan would be here to guide them. Suddenly, a shadowy figure appears. Runo then has a flashback of when she was small with Dan. Then Lars Lion transforms into an old lady and awaits for Runo in a cave. Wondering where they are, the duo stumbles into an old lady. The lady suggests some directions, but Runo is creeped out by her looks and ponders deeper into the woods.

After cluelessly strolling in the forest, Runo encounters a little boy. The little boy was in a hurry and steamed off to somewhere. Desperately needing directions, Runo and Tigrerra decide to chase after him. As the two were catching up to him, Runo has the strangest feeling that she has seen the little boy before.

Dan and the rest of the Brawlers return home back to Earth from the Doom Dimension, but Dan is unsure how to tell them that he didn't pass his test yet or how he needs to battle all of them in order to do so. Meanwhile, Joe & Wavern are challenged by Masquerade, who wants the Infinity Core from Wavern.

Joe reveals that he and Wavern defeated Masquerade thanks to the vast positive energy and power of the Infinity Core. Drago and Wavern also reveal that they were in quite a strong and close romantic relationship in Vestroia. Dan and Drago reveal to the Shun, Marucho, Julie and their bakugan that they didn't pass their test.

Alice finally returns and her memories are all hazy as to where she has been. As Runo comforts her, Alice says she feels like she's become a different person. After that, all the Brawlers minus Alice are over at Dan's watching the news reports about all the strange weather occurring around the world, then out of the blue Joe is challenged by Masquerade to a battle for control of the Infinity Core. Dan's decides to take on Masquerade in Joe's place because Drago has evolved into an Ultimate Bakugan. Meanwhile at Runo's, Alice has disappeared again. Dan and Masquerade meet and the others realize that it will be a battle between the first and second ranked Brawlers. When the battle begins, the Brawlers learn that Dual Hydranoid has evolved into Alpha Hydranoid and Masquerade learns that Drago has evolved into Ultimate Dragonoid. The battle wages on and neither side is giving way, resulting in several consecutive draws, but the battle arena is slowly being destroyed by the clashing powers of two powerful Bakugan. In the end though, Dan and Drago end up the winners.

Klaus flies Alice to the Vestroia portal, where as she jumps and skydives toward it, she summons Masquerade's mask and transforms into him one last time to get his support to help Dan and Drago. Masquerade and Hydranoid arrive just in time to save Dan and Drago from Centorrior and Druman. Knowing that without a plan, they won't be able to win, the duo retreat. They come up with a plan to take out Druman and Centorrior. Everything begins to go as planned, with Drago luring Druman while Hydranoid gets Centorrior's attention. All is well when Centorrior and Druman are in range of the gate card, and Masquerade activates the gate card and the two are slowly defeated. Suddenly the plan crumbles and falls apart as Druman destroys the gate card. Drago then attacks Druman, although Druman reflects the attack, bouncing off and hitting Hydranoid, causing Masquerade and Alpha Hydranoid to fall off the cliff and the Battle Brawlers look like they have failed. The battle rages on as Drago tries to get Druman and Centorrior to a specific area.

As the Brawlers reach the center of Vestroia, they discover that Naga is no longer there. Meanwhile, Naga appears on Earth to move onto the next phase of his plans. Naga closes the portal that connects Vestroia to Earth, a portal he opened to deliberately lead the Brawlers into and then he begins to open more portals around the world to let in his Bakugan army. Naga's ultimate goal is to capture Wavern and to take the Infinity Core and with the Brawlers out of the picture, it looks like he will succeed. But, Joe doesn't give up and sends a message for help to any and all brawlers willing to fight against Naga and his minions. Battlers from all over the world, including top brawlers Chan Lee, Klaus Von Herzon, Billy Gilbert, Komba O'Charlie, and Julio Santana, answer Joe's message and with their Bakugan, go on the offensive against Naga and his team. Komba and Harpus lead one group of battlers against Tayghen, while Julio and Tentaclear lead another group against Tricloid, and Billy leads a third team against Rabeeder.

Naga's troops have finally infiltrated Wardington after being defeated twice already. Alice discovers that Tricloid's sister Rabeeder is invading the town. Little does she know the one she trained before, Christopher, will also get involved in the battle. Dan is informed that Hairadee, Centorrior and Druman are also approaching the city following Tayghen's death and Tricloid's defeat. When it appears these two are being overpowered, Klaus arrives.

Drago and Naga's battle continues, until the Brawlers step forward, launching their Bakugan into battle to reinforce Drago. With the power of all six attributes, Drago overwhelms Naga and destroys him, releasing the Silent Core and absorbing it. Upon Naga's demise, Hal-G is also destroyed, reuniting Alice with her grandfather, Dr. Michael.

With the battle over and the world saved, it is time for the Brawlers and their beloved Bakugan to say goodbye. After the group shares a tearful farewell, Drago opens a portal to Vestroia, allowing all Bakugan to begin their journey home. Sacrificing himself, Drago becomes the core of New Vestroia itself, restoring the Bakugan homeworld to its original state. With the Bakugan gone, everything eventually returns to normal.