It's an all new adventure for the Bakugan Battle Brawlers when Dan's family moves to Bayview City and Marucho's Bakugan Interspace becomes fully operational to everyone, allowing kids all over the world to log on and display their battling skills. Dan heads to a cafe in town where Julie works to meet with his new friend Jake, a young brawler who is new to the game. The two make there way to Bakugan Interspace where they meet up with Marucho who gives Jake Subterra Coredem

On the distant planet Gundalia, the Twelve Orders discuss the explosion caused by Ren and Dan's battle in Bakugan Interspace. Kazarina, the head of the Bakugan Biology Research lab, is unable to identify the strong powerful Bakugan that caused the explosion. So, Emperor Barodius orders that this bakugan be brought to them before it joins their enemy

As Ren identifies three more Neathian moles (Mason Brown, Jesse Glenn, and Zenet Surrow), Princess Fabia from Neathia arrives in Bakugan Interspace looking for the recipients of the message she sent. Dan, having slept in, rushes to Bakugan Interspace and runs into Fabia, literally. Fabia learns that he is the top brawler in Bakugan Interspace, but before she can ask about her message, Dan rushes off to meet his friends

Dan gives Jake a practice match, but Jake feels he is not ready to become an official Bakugan Battle Brawler. When another mole, Mason Brown, is located, Dan challenges him to a battle, but Jake steps in and wants to prove himself. Due to his inexperience, Jake quickly loses and feels he has failed Dan in proving himself

With the Neathian moles making themselves known, they begin kidnapping brawlers from Bakugan Interspace. The puzzling part is that each brawler is eventually returned to BI. Meanwhile, Sid and Zenet find their recruiting hard when Marucho puts out an announcement to everyone not to battle Sid, Lena, Mason, Jesse and Zenet

Fabia tells Shun her side of the story, which he believes while he worries that the others have made a big mistake. While Marucho and Ren work hard on an expansion for Bakugan Interspace Jesse Glenn arrives. Dan heads to the new arena to challenge him but is stopped by Fabia, who claims that Jesse is not who he claims to be

Marucho frantically searches Bakugan Interspace and his home for Ren, but comes up with nothing. Meanwhile, Ren meets up with Sid, Lena, Mason, Jesse and Zenet, scolding Jesse for giving away his cover. Marucho uses a secret message to get Ren to meet him and they battle

After the battle with Ren, Marucho is refreshed and even constructs a speech program for the clone Akwimos. Fabia worries that Dan and the others do not fully trust her as they were easily tricked by Ren. Dan assures her that they completely trust her after seeing how angry she got about Bakugan being used for war

Dan and the others have been forced out of Bakugan Interspace and Ren has taken control! However it seems that they were the only ones kicked out as other kids continue to log on, not knowing what is going on. To make things easier, Marucho, Shun and Fabia head over to Dan in Bayview City aboard his giant airship. Dan tries to enter Bakugan Interspace, but is rejected

With Ren still under control of Bakugan Interspace, Marucho quickly comes up with a plan to regain his beloved creation. Emperor Barodius calls Ren and suspects Ren may betray them due to his desire to not battle with his former friends. Ren assures him of his loyalty while Linehalt attempts to get the truth from his friend

The Gundalians are easily overpowering the Neathians thanks to the brainwashed brawlers Ren got from Bakugan Interspace. In a last desperate attempt, the Captain of the Neathian Guard sends a Castle Knight, Linus to Earth to give Fabia the Element, the very thing the Gundalians are trying to take from the Neathians. As security tightens for the brawlers, their attempt to bring kids out safely is getting more difficult

Dan and the others devise a plan to regain Neo while Linus desperately struggles to rescue his friend. Far too injured from the previous episode, Dan urges Linus to rest and leave rescuing Neo to him. With the Gundalian's search for the Element comes up with nothing, Ren is given orders to bring Neo to Gundalia on suspicion that he holds the Element

With Drago receiving the Element from the now departed Neo, the Brawlers decide to head back to Neathia to help fight off the Gundalians. Before they can do so, Dan must say goodbye to Julie, who hastily borrows his bike to get to her cheerleading practice. Meanwhile, Ren sends Zenet to steal the Element back via trickery

As the Brawlers arrive on Neathia, Fabia introduces them to her older sister, Queen Serena. She then takes the brawlers to see the Sacred Orb, the true target of Barodious' conquest. Shun asks her whether it was this or the Element Barodius was after to which she replies that the Element was merely a portion of the Sacred Orbs power and that the Sacred Orb is the real target

With only one shield left defending Neathia, it looks like Gundalia may actually win this war. However, Marucho devises a plan to distract the oncoming Gundalian attack consisting of Airzel, Kazarina and Stoica, while a small unit consisting of Shun, Dan, Fabia and their Bakugan head to the second shield generator to restart it. Marucho and Jake act as the decoys while Fabia leads Dan and Shun to the generator

With only one shield left defending Neathia, it looks like Gundalia may actually win this war. However, Marucho devises a plan to distract the oncoming Gundalian attack consisting of Airzel, Kazarina and Stoica, while a small unit consisting of Shun, Dan, Fabia and their bakugan head to the second shield generator to restart it. Marucho and Jake act as the decoys while Fabia leads Dan and Shun to the generator

Shun successfully sneaks past the Gundalian guards into the second shield generator, but is ambushed by Lena and Kazarina. A battle quickly ensues and Lena is taken out and berated by Kazarina. When she and Lumagrowl begin giving Shun too much trouble, Dan and Hawktor suddenly arrive to save the day! Dan and Shun switch back their bakugan and Shun heads to the generator while Dan holds off Kazarina

While the brawlers help the Neathians rebuild, Jake has an argument with Dan, saying that they should keep pressing the attack on the Gundalians now that they have the advantage. When Dan and Marucho argue that they should help rebuild, Jake runs off into the forest, followed by Fabia. Meanwhile, Jesse fears that he will eventually suffer the same fate as Sid and Lena and escapes from his prison to Neathia

With the second shield functioning at an even more powerful rate than before, things are looking good for Neathia. Meanwhile, Nurzak and Kazarina are sent to do recon. Nurzak tells Sabator how Barodius' father, the previous Emperor, did not seek to attain the Sacred Orb, fearing that its power is too great, while Barodius is far too ambitious and down right stupid for engaging in such a quest

The brawlers decide to use the Sacred Orb to their advantage by convincing Gundalians who fear it's power to switch sides, namely Nurzak. Ren has a meeting with Barodius where the Emperor reveals that despite the failures of Ren's team, he keeps Ren around because of his potential. Later in the hallway, Linehalt asks Ren what is wrong, to which he replies the only reason they serve and obey the Emperor is because he was allowed out of the darkness he and Linehalt had lived in

Nurzak sends a message to the brawlers for a meeting to discuss a peace treaty. The brawlers are unsure but decide to take the risk anyway. Nurzak plans to use Kazarina's attack on the emperor as his chance to sneak away to Neathia and give the brawlers the Switch Code, something that can supposedly control the Sacred Orb

With one of the 12 Orders disposed of, Barodius secures the loyalty of the others or else they will face the same fate as Nurzak. 2-3 days are required before Dharak's Exokor is ready, so Dharak suggests that, in the meantime, they launch a smaller attack to distract the Neathians. Once again, the Gundalians rely on the kidnapped humans from Bakugan Interspace to do their fighting for them

Deep within Gundalia, Sid wakes up from statis and learns that he, Lena, Jesse and Zenet were not actually killed, but imprisoned. Barodius order the attack to commence at dawn while Kazarina continues with her experiments. Sid has managed to escape and notices Ren leaving with some troops

After his battle with Dan and Sid giving him Rubanoid, Ren is very confused as to what he should do. The invasion continues on as the brawlers continue to push back the Gundalians. Kazarina finishes her experiments on Dharak's Exokor while Ren visits Barodius

Ren decideds he has had enough of Barodius' false promises and turns on him to fight by his true friends. Dharak however, chooses to let Exokor, Riptor, and Smashtor do the fighting, but eventually joins in a one on one battle against Linehalt. Meanwhile, one by one, the brawlers are taken out by the Twelve Orders (Although Shun managed to take out Kazarina before falling to Airzel)

With Ren back on the team, everyone heads back to Neathia, but discover that Ren has been left behind! Elright explains that, as a last resort, the third shield is programmed to expel anyone with Gundalian DNA. Dan asks if they can just shut the shield off to let Ren in, but Fabia refuses and leaves. Serena explains the origins of her hatred to the Gundalians: Aranaut was originally partnered with Commander Jin, but they were defeated by Kazarina

Soon after Ren joined the Castle Knights, the Gundalians begin attacking the third shield. When they find that the third shield contains a DNA barrier, they retreat back to Gundalia for a new strategy. Meanwhile, the Neathians send out patrols to watch out for any Gundalians attacking while a geometric storm (something that disrupts their radars) is taking place, with the Brawlers divided into groups of two to help the patrols

Jake has been captured by Kazarina and is tortured by her. Meanwhile, Dan eagerly wants to rescue him, feeling that their argument was his fault but everyone tries to talk him out of it. Just then Jake suddenly walks right back into Neathia, claiming to have escaped, however, Shun is not easily convinced of this

Dan is still upset about losing Jake and wants to rescue him, but Queen Serena forbids it, as it is too dangerous. Frustrated, Dan recalls the day he first met Jake. Linus arrives to bring them all lunch, when Dan and Drago are suddenly pulled away by Dragnoid Colossus to a place between dimensions

While the Brawlers are on their way to Gundalia, Ren tells the others that he wishes to save the rest of his team from Kazarina's lab, to which the other Brawlers agree. Ren, Fabia, Mason, and Nurzak split off from the rest of the team to rescue them. Dan, Marucho and Shun make their way inside the palace to find Jake

Dan and Barodius immediately battle with Drago easily tearing through Dharak's Exokor. However, Dragonoid Colossus informs Dan that Drago and Dharak are too evenly matched and that Drago must win at all costs. Despite another evolution, it seems as though Drago barely matches up to Dharak in terms of power

Dan is caught off guard by Jake and is imprisoned in a cell that keeps Drago in ball form. Meanwhile, Fabia and Nurzak engage in battle with Kazarina and Stoica, giving Ren and Mason a chance to break in and rescue Zenet, Lena and Jesse. However, once they reach the lab, they are nowhere to be seen

With Dan and Drago captured, Kazarina discovers similarities between Drago and Dharak's DNA and discovers a way to use that DNA to make Dharak evolve. Fabia informs Ren and Mason about Jesse, Lena, and Zenet being hypnotized so Mason takes them to Nurzak's secret lair. Meanwhile, Shun and Marucho split up to find Dan and Jake

Ren and Fabia reunite with Shun and Marucho and regroup with Mason at Nurzak's secret lair. Meanwhile, Kazarina's experiments have succeeded and she is ready to splice Drago's DNA with Dharak's. This results in Dharak evolving into Phantom Dharak as well as his DNA no longer containing Gundalian DNA, allowing him to pass the third shield

Just as Kazarina is about to finish Dan off, Jake breaks free of the hypnosis and stops her. Fabia arrives and holds off Lumagrowl while Jake and Coredem rescue Dan and Drago. During the battle, Kazarina and Lumagrowl reveal Aranaut's last time on Gundalia: when Jin was killed and he was captured

The brawlers must head back to Neathia to defend it from Dharak's attack but Kazarina, Stoica, Gill and Airzel are determined to keep them on Gundalia. The brawlers manage to fight them off and escape, but Fabia remains behind to fight Kazarina, as she has a vendetta against her for the death of her fiance, Jin. The brawlers quickly make their way back to Neathia, with the Gundalian forces close behind, as Elright and Linus who has Rubanoid as his partner attempt to fight back

Just as the Brawlers return to Neathia, Fabia and Kazarina continue their battle. However, Lumagrowl begins disobeying Kazarina's orders and is determined to finish off Aranaut with or without her.

Nurzak, Mason and Fabia attempt to return to Neathia on Nurzak's ship but they are stopped by Gill, though they do manage to escape and arrive just in time to help the brawlers. Lena, Zenet and Jesse are surprised to see Nurzak and Maron alive, but are nonetheless happy. Gill arrives on the scene and tries to convince Barodius that Fabia killed Kazarina, however, Barodius knows it was Gill who killed her and shoots down his ship, along with Airzel who tried to save him

Code Eve explains that in the beginning, Dragonoid and Dharaknoid had battled each other and the result split the universe in two (Dragonoid's half formed into Vestroia and Dharaknoid's half created Neathia and Gundalia) which is why she had brought them to a mid dimension to battle, so no innocents would come to harm. Drago struggles against Dharak, and is knocked out and reverts to a primal state, relying solely on instinct, but Dan manages to snap him out of it. Meanwhile, everyone awakens after being defeated by Dharak and Linehalt is upset at the devastation so he uses his Forbidden Power to restore the war torn Neathia