Wayvern is calling to Drago to tell him that she needs help, the top ranked Brawlers must defeat Centorrior and Druman. Meanwhile Naga's negative energy is proving to be too much for Wayvern and Fortress. With Centorrior defeated, the others deal with Druman as Dan and Drago head over to where Naga. When Drago arrives, he fights Naga. With help from Julios, Runo has Tigrerra destroy Druman. Wayvern asks Drago to attack her so she can give him the Infinity Core. He does so, and Wyvern disappears. Drago becomes Infinity Drago. Drago then continues his fight with Naga. They both have 1000 Gs. In an epic battle, the two seem evenly matched. However, Hal-G sends out his 5th Paladins to assist Naga.

As Hal-G releases 5th Paladins, all seems hopeless until the Brawlers send their Bakugan to aid a wounded Drago. They destroy the 5th Paladins as Naga absorbs the 5th Paladins' energies. With the last of his power, Drago fires a brilliant burst of fire.

Hydron discovers that a fellow prisoner is none other than Gus Grav, who was presumed dead in episode 39. Meanwhile, Runo, Julie and Mira prepare a cake for Keith to officially celebrate his joining the Resistance. However, Keith's mind lingers elsewhere, something that Mira notices but Keith brushes off. Dan suggests that instead of waiting for Zenoheld's attack, they storm the palace. Keith, however, is too impatient and takes his ship to the Vest Palace on his own. A battle quickly ensues and Gus feels Spectra needs his help, so he tricks Hydron into battling so their bakugan can free them from their cells and Gus leaves to help Spectra while Hydron is left on his own. When Zenoheld nearly defeats Spectra, Gus arrives in the nick of time, shocking Spectra who is happy finding out that Gus had survived. The two then battle together, giving them the upper hand against Zenoheld. Partway through the battle, Prof. Clay informs Zenoheld that the Alternative System, a giant airship modeled after Farbros, is complete and targets Spectra and Helios for a test fire. The blast sends Spectra's ship flying and takes a huge chunk out of a small planetoid, with Spectra and Gus just barely escaping the impact. Farbros links with the Alternative System and King Zenoheld declares his quest for intergalactic domination to begin.

With Keith having gone to the palace and having no way to find said palace, the Resistance are stuck. Luckily Alice and Dr. Michael arrive and use the teleportation signature left behind by Shadow and Mylene to back track to the palace. Meanwhile, Zenoheld continues his attack, forcing Spectra and Gus to retreat and come up with a plan of counter attack. The Resistance are saddened to hear that Tigrerra and Gorem do not wish to participate on the assault of the palace due to the fact that they know their limitations (which are lower than the rest of the team) and it would irresponsibly put Runo and Julie in danger. All of a sudden, Dr. Michael locks onto the palace's coordinates and the Resistance - minus Runo, Julie and Alice - head for the battle and arrive just in time to see Helios and Vulcan in trouble. However, the Alternative is far more powerful than any of them could have ever imagined (because despite the amount of damage they did, which was a pretty decent amount, the Alternative still repaired itself with Farbros). Keith realizes that because Prof. Clay built the Alternative, that he must be inside and asks Mira if she wants to confront him, which she does. Then, Keith uses a new battle gear, the Zukanator, on Helios, in hopes that it will even out the playing field. Keith blows a hole in the Alternative and he and Mira enter the machine.

With the battle against the Alternative pressing on, Hydron shows up to lend a hand. Meanwhile, Prof. Clay receives a video transmisson from a faraway world just as Mira and Keith arrive to make one final appeal. Once the brawlers realize Mira and Keith are missing, they deduce that the siblings may have found a way inside, so Dan uses Jetkor to blast a hole in the Alternative while Gus and Marucho stay behind to guard the rear. Gus and Vulcan are nearly beaten when Hydron steps in and saves him. Shun, having suggested to find the Power Reactor of the Alternative AND having memorized the blueprints of the machine, leads the Resistance through the Alternative. However, they are all quickly caught in a trap against four mysterious bakugan, unrecognized by Drago. While Mira pleads with her father to abandon his evil plans with Zenoheld, Dan and the others destroy the four unknown Bakugan as well as the Power Reactor. As they make their escape, Prof. Clay saves Mira from falling debris, but is trapped on the ship and Hydron captures his father, forcing them both to "go down with the ship." Prof. Clay returns to this computer and finds that the video he received depicts Bakugan in war. The Resistance go their separate ways as Keith and Gus thank Dan for showing them the error of their ways. 3 weeks later, Marucho has completely repaired Bakugan Interspace and uses Akwimos to test it while Shun uses Hawktor and Dan sticks with Drago. Then, they are approached by a boy named Ren who asks them if they're the Brawlers.

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. Dan and Jake immediately want to battle, but discover that all the available arenas are occupied. They eventually meet up with Ren and Shun, who is locked in battle with Shuji. With Shun quickly seizing victory, Ren is scheduled to battle Dan next. As the battle intensifies, Marucho is forced to shut down Bakugan Interspace and Dan is knocked out cold. Before coming to, Dan has a vision of Bakugan at war each other, something which everyone, except Ren, brushes off as a hallucination.

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. Back on Earth, Jake and Julie still believe that what Dan saw was a dream, though he is still convinced that it was real. Just then, Marucho calls and everyone heads to Bakugan Interspace, where Ren confesses that he is a humanoid alien being from Gundalia looking for strong battlers to help fend of the invading Neathians. Though hesitant, the Brawlers accept and track down two moles identified by Ren, Sid Arcale and Lena Isis and a battle ensues. Though Sid and Lena gain the upperhand, Dan pulls through with Jetkor and wins the battle. Everyone congratulates Dan on the victory. However, there may be more to Ren than meets the eye.

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. He tells them about the girl and Ren suspects she may be a Neathian spy. Before they can track her, Fabia arrives and is shocked to find that Ren, a Gundalian has gained their trust first! Now that Dan has sided with the Gundalians, Fabia claims they are her enemy and a battle ensues between her and Dan. Dan quickly takes the lead but falters when Fabia summons Haos Aranaut, the original Aranaut from which the clone Aranaut, Coredom, Hawktor and Akwimos originated, meaning Fabia sent the Phantom Data. This also means that it came from their enemies, the Neathians, something that Shun is not so sure of anymore. Defeated, Fabia leaves and wonders what to do now that Dan has sided with the Gundalians. While the others congratulate Dan on his victory, Shun disappears to ask Fabia what her side of the story is.

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. The next day, Jake is still upset over his loss, so Julie, being a Subterra master, offers to help him discover his own battling style. Jake returns for a rematch with Mason while being greeted by a bitter crowd. With his newfound confidence, Jake easily defeats Mason. Before the Brawlers can pursue Mason, he teleports out of the stadium. Dan congratulates Jake, who becomes an official Battle Brawler.

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. In retaliation, Sid and Zenet challenge Dan and Ren to a battle. Ren is quickly taken out, leaving Dan to fend for himself. Being outnumbered, Dan loses but Sid allows him to keep Drago. After the battle, Gill of the Twelve Orders orders Sid to not engage the brawlers and to leave it to Ren, who states their plan is working perfectly.

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. Fabia steps in to fight Jesse, something that greatly confuses Dan and the others since they all think that both Jessie and Fabia are Neathians. Ren insists that they do not cheer for either of them and they should just let their enemies destroy each other. Despite this, Dan, Jake and Marucho cheer for Fabia. Although she puts up a good fight, Fabia loses due to a bug in the field, causing her to cry over her loss. Shun explains that the only person who could plant an unlikely bug that caused Fabia's defeat was someone familiar with the BI System, someone like Ren. Ren denies everything while Jesse flees. Fabia and Shun expose Ren for lying about how Neathia attacked Gundalia, causing him to run away. Marucho, however, refuses to believe these accusations and rushed off to find Ren.

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. Meanwhile, Fabia tells everyone her side of the story. Neathia was attacked by Gundalia and, due to their bakugan's inexperience in battle, they quickly lost to the Gundalian Bakugan. Fabia then sent out a distress message via the Phantom Data which lead her to BI on Earth. Shun discovers the battle going on between Marucho and Ren. When they arrive, Marucho defeats Ren. Ren attempts to get Marucho to switch sides, but he refuses to leave his friends. Ren declares their friendship over and reveals his true Gundalian form and tells Marucho that the next time they meet, they will be enemies.

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. Relieved, Fabia gives Shun, Marucho and Jake the real Hawktor, Akwimos and Coredem. Meanwhile, Ren leads the other Gundalians to kidnapped two brawlers named Taylor and Casey. The two are taken back to Gundalia where they are brainwashed into fighting against the Neathians. Dan and the others confront Ren who sends Taylor and Casey to attack them. Dan and Shun battle Mason and Taylor while Marucho and Jake battle Sid and Casey. Fabia, however, sneaks off in hopes for finding Ren to discover his plans. After winning their respective battles and freeing Taylor and Casey from the Gundalians' control, they are all forced out of BI. Ren reveals that he is now in sole control of BI.

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. He tries to tell the other kids about the danger, but none of them believe him. Marucho is unable to shut it down as Ren has complete control, so Jake tries brute force, which actually works. Marucho takes them to a remote access room so they can plan their next move. Fabia remembers that the Neathian Bakugan can body shift themselves into Interspace. Dan immediately wants to go, but Drago reminds him he does not have that same power. So Jake volunteers and brings Dan along using Coredem's power. Dan and Jake witness brainwashed kids take back more kids back to Gundalia. The same two brawlers who accused Dan of lying reappear, now brainwashed by Gundalia, and battle Dan and Jake. They easily secure victory as well as the opponent Bakugan. The two boys are released from Gundalian control and Dan and Jake take them out of Bakugan Interspace. Dan vows to rescue all the brainwashed children.

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. Ren reminds him of the story behind their loyalty to Barodius: there were many ancient Bakugan with Forbidden powers but they were sealed underground. Eventually their numbers dwindled to just Linehalt. Ren was the last descendant of the Protectors of the Dark Bakugan and was assigned to take care of Linehalt. Over the years, they bonded and dreamed of escaping their underground prison until Barodius recruited them to lead the invasion team to Earth. Meanwhile, Marucho and Fabia infiltrate Bakugan Interspace. Marucho tries to regain control while Fabia and an Avatar Marucho battle Lena and Zenet. The Avatar is quickly taken out as Ren discovers Marucho's invasion. Fabia is defeated and Zenet and Lena decided to take her back as a prisoner, something that will give them an edge against Neathia. However, Marucho arrives in time to get her out. Though their mission was unsuccessful, Marucho reveals he installed a back door to better access Bakugan Interspace without alerting Ren and his team.

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. However, many of the kids believe Dan and the brawlers over their wanted announcement. After Shun returns from saving more kids, he runs into Linus who is looking for Fabia. Though reluctant to trust him at first, they are attacked by Ren and Jesse and a battle ensues. Linus' partner Neo displays incredible power but the battle eventually goes to Jesse, who takes Neo as his victory prize. Linus is taken back to the others after being injured during the battle. He tells Fabia that having lost Neo to the Gundalians, he has also lost the Element, leaving Neathia doomed.

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. Before Ren can carry out these orders, Sid barges in and takes Neo, deciding to get a little glory himself and challenges Dan. When Sid finally throws in Neo, Neo gives Drago the Element, causing him to evolve into Lumino Dragonoid. However, Neo's body disappears in the process. With Drago evolving once again, Dan easily takes a win. Meanwhile, Neo appears to Linus in his dream to bid his friend a final farewell, his mission now complete. Julie comes into the room to find Linus crying over the loss of his best friend. Ren and Sid are berated for having lost the Element so soon after getting it. Sid's Rubanoid is taken by Kazarina for experiments while Sid is disposed of. Ren pleads for another chance, which the Emperor grants but implores Ren not to "test" him anymore, this was Ren's final chance to prove himself to the Emperor.

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. So, she disguises herself as Julie and tries to take Drago. However, her plan is foiled when the real Julie shows up, throwing Dan and Drago into confusion! However, when he reveals he is leaving for Neathia to help fight, the real Julie expresses that she is ok with it and hopes they succeed, assuring Dan that she is the real Julie. Zenet is forced to reveal herself and battles Drago. She tries to trick Drago by transforming Contestir's appearance, but Drago overpowers her with his new Battle Gear Cross Buster. Zenet retreats and informs Ren that the Brawlers are heading to Neathia. Ren runs to them before they go, but arrives just as they leave with Julie cheering them on, commenting that they will meet soon again.

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. Meanwhile, Barodious scolds Ren, Lena, Zenet, Mason and Jesse for seriously failing their initial plan to gain the Brawlers' trust and violenty commands the Twelve Orders to attack Neathia. The Brawlers do their best to hold the Gundalians off while Dan and Drago fight Barodius and Dharak Colossus but they succeed in breaking through Neathia's second shield. While the fighting is going on, Captain Elright, who was captured in episode 11, escapes from one of Gundalian's Stabber Knights and joins the battle. Just before Drago and Dharak can engage in further combat, the Sacred Orb suddenly teleports all the Gundalians away. The Neathians celebrate their victory as Fabia, Dan, Jake, Marucho, and Shun are made Castle Knights, the highest honor on the planet Neathia.

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. When the battle gets too intense, Marucho and Akwimos trap Strikeflier and Avoir in ice and escape, while Fabia, Dan and Shun get closer 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. When the battle gets too intense, Marucho and Akwimos trap Strikeflier and Avoir in ice and escape, while Fabia, Dan and Shun get closer 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. Shun reactivates the shield as Drago powers it up with the Element. Realizing what is happening, Airzel, Stoica and Kazarina quickly flee before being trapped within the shield. As the brawlers celebrate their victory, all is not well on Gundalia. Kazarina knows she will be punished by Baridous for the failure, so she plans to use Lena as her scapegoat. Lena, however, is fully aware of this thanks to Gill, and attempts to get Phosphos to assassinate Kazarina before it can happen. Unfortunately for her, Kazarina is well prepared Phosphos is taken out by Lumagrowl while Kazarina disposes of Lena. Kazarina successfully blames Lena for the failure and speaks to Gill about how Lena somehow knew of her plan, suggesting that she knew Gill had tipped her off. Gill remarks that not everyone can be trusted in these hard times...while Ren overhears their conversation and silently apologizes to Lena for her fate.

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. He is eventually approached by Ren, who has been sent to collect him. They eventually run into Jake and Fabia and a battle ensues, Jesse promising that he will return with Ren no matter how the battle concludes. Jake and Fabia defeat the Gundalians and Jesse willingly returns to Gundalia with Ren, having had one final battle. Kazarina and Stoica prepare to punish Jesse for his escape and lose to the brawlers while Ren attempts to spare Jesse by saying he was much a part of the battle as Jesse was. Kazarina, however, tells him that he can share that information with Barodius himself. Plitheon suddenly speaks out and begs to be separated from Jesse, declaring that he can't stand him, something that surprises Jesse. However, Lumagrowl and Lytherius attack Plitheon for turning on his master. Jesse forgives Plitheon, saying that co-stars often have friction between them, but Plitheon insists he means what he said, as he slowly fades away. Jesse remarks that the spotlight is on Ren now and is presumed killed, leaving behind the book he always carries. While Kazarina and Stoica are walking through the hall, Nurzak appears and tells them that although they can trick the others of their true intentions, he can see them for what they really are.

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. Mason, however, has plans of his own and escapes the ship, possibly to switch sides. Kazarina becomes infuriated because of what may happen to her, but Nurzak assures her that he and Ren will find Mason. While on their search, they run into Fabia and Marucho, who still feels bitter about Ren's betrayal. Marucho's emotions only become worse when Ren says that their entire friendship was just a ploy and that Marucho shouldn't let something so stupid affect him so. The battle becomes so intense that the Sacred Orb shoots out dimensional rays, that should one get caught in, they will be sent around the dimensions without any way back. Nurzak and Ren retreat while Aranaut and Akwimos attempt to shield Fabia and Marucho from the dimensional rays. Just before it hits them, the Sacred Orb stops but not before Mason and Avior fall victim to it. Back at the palace, Serena expresses how happy she is that Fabia and Marucho made it back all right, while everyone questions why the Sacred Orb acted so. Meanwhile, Marucho believes that Ren will return to their side. However, things don't look to good for Kazarina as she finally gets the punishment she deserves from Barodius, though she is kept alive. While in the hallway, she encounters Nurzak who tells her that he is leaving the Emperor and with Gill as the Emperor's right hand, she needs to find a place for herself quickly. He encourages her to join him, to which she agrees.

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. Suddenly, Zenet comes in and begs Ren to help her, fearing that she will suffer the same fate as the others. Ren brushes her off and tells her she has nothing to worry about. However, she is not convinced. Contestir tries to cheer her up by agreeing with Ren, but Zenet tells him that Gundalians care nothing of loyalty and despite her morphing abilities she has no use to them. Then she overhears that Gill and Ren are leaving to Neathia to destroy the second shield again. She disguises herself as Ren to take his place in order to prove herself, but Krakix easily sees through the guise and Gill decides to give her a chance anyway. While Gill and Krakix gather data on the second shield to completely destroy it, Zenet must keep Shun and Hawktor off him. However, Shun proves to be too much for her to handle, so Gill steps in and nearly defeats Shun, that is until Dan and Drago arrive. Gill and Zenet are defeated and return to Gundalia, where Zenet greatly fears her punishment. However, Contestir convinces Gill that because he is Barodius' right hand man, he will likely have people plotting against him, and that he may have use for a spy and volunteers Zenet. Gill sees this as a good idea and sends her to spy on Kazarina as Nurzak. She pulls it off and returns with information that Kazarina and Nurzak and plotting to overthrow the Emperor. Despite a job well done, Gill and Krakix kill Zenet and Contestir. Zenet once again explains Contestir that Gundalians care nothing for loyalty. Contestir argues that he has always been loyal to Zenet. She begins crying and apologizes for not seeing it earlier.