Kenta, a young boy after winning a beyblade, Sagittario, runs into a band of bullies called the 'Face Hunters' who bully him to play an unfair match. Kenta unexpectedly is saved by Gingka, the main protagonist with his beyblade Pegasus and wipes out the beys of The Face Hunters easily. Benkei, who is second in command of the gang challenges Gingka that he is going to regret this and runs away. Later, Gingka and Kenta become friends and Gingka tells Kenta that he is exploring the country to find challenging opponents and improve his bey powers. Next morning, Benkei invites Gingka to the Face Hunters and accepts it readily and is challenged by 100 bladers but he defeats them with equal ease. Soon, Kyoya steps up revealing that he is the Face Hunters leader and would like to have Gingka as an opponent and challenges him to battle.

Kyoya, leader of the Face Hunters, has challenged Gingka. Gingka and Kenta discuss this challenge. Kenta even introduces Gingka to his fiends and tells them about his feat to defeat the Face Hunters. Outside, Madoka, a young girl announces that Gingka's bey Pegasus is in need of repair. She explains that dust, scratches and other things damage a bey and it cannot be used to its fullest and proposes to repair the beyblade of Gingka for free. Gingka worries about the match between him and Kyoya and if he should give his beyblade Pegasus to Madoka for repair. But eventually he does and Madoka repairs it, but on the day of battle with Kyoya, Madoka says that the balance of the bey remains unrepaired but Gingka takes the bey and battles Kyoya crushing his wind storm and defeating him with his special move. Later a silhouetted figure appears and claims he can defeat Gingka.

Doji takes Kyoya away from the city to make a deal. If Kyoya loses a battle against him then he must go with him. Meanwhile Kenta is worried Gingka is getting bored with having no strong opponents to battle and challenges him to prove his worth.

Doji gives Benkei a new bey, Dark Bull, with which he can defeat Gingka. Excited, Benkei sends Kenta off with a challenge for Gingka. Upon arriving, Gingka and co realized strange holes have been made at the battle location, and then a bey appears. Gingka and co follow the bey to Benkei, where a heated battle ensues. As the battle continues the warehouse begins to fall apart, and soon the ceiling above Gingka collapses, but Benkei selflessly saves Gingka, as well as providing comic relief due to his lack of reasons on why he did that.

There's a new blader in town, Tetsuya, who is destroying the beys of the bladers he defeats. Angered by this, Madoka sets off to find him with Gingka and Kenta in pursuit. After splitting up, Kenta realizes one of his friends is a new victim of Tetsuya. He battles him, thankfully saved by the arrival of Gingka. But Tetsuya has kidnapped Madoka, and unless Gingka defeats him, she'll remain missing.

Hikaru Hasama, a strong blader from afar, arrives in town and is asked by Benkei to defeat Gingka. Meanwhile, Kenta wonders whether Sagittario could have a special move, Madoka explaining it's possible. Hikaru accepts Benkei's offer, but Gingka is sick and so Kenta battles in his place, unbeknown to Hikaru.

Kenta is trained by Benkei to defeat Hikaru whilst Madoka gives Kenta a new bey part to help him with his special move. Meanwhile, Hikaru has been told by Tetsuya who her real opponent was and is on the prowl for the real Gingka Hagane, though is interrupted by Kenta.

Kyoya is sent to Wolf Canyon by Doji to test his skills. Meanwhile, Merci kidnaps Gingka and convinces him he's on a TV show while it's really testing his skills.

Kyoya has returned from Wolf Canyon and Benkei is excited to see his old friend again, with encouragement from Kenta. But Kyoya has changed, revealed in a battle, and even with Kenta at his side Benkei loses as Leone destroys the warehouse they're in.

Kenta returns with an injured Benkei and tells Gingka what Kyoya did to them. Furious, Gingka challenges Kyoya who is now out of control, bent on destroying Gingka and Pegasus. During the battle, a tornado rips through the city, involuntarily summoning his friends to cheer him on. The battle is a fierce one, but Gingka wins, bringing Kyoya back to his senses. Suddenly, they all spot a conspicuous-looking helicopter bearing the seal of Gingka's sworn enemy, the Dark Nebula, led by Doji.

Gingka returns and explains to his friends that Doji has a forbidden bey: Lightning L-Drago. Tipped off by Kyoya, they arrive at the Dark Nebula castle and are ambushed by many beys. With help once again from Kyoya, they break down the doors and head inside, for what will be a long battle to the top.

After many challenges, Gingka is the only one to reach Doji. They battle which causes one of the walls to collapse. But their challenge isn't over yet...

Ryuga, an old rival of Gingka's and the new owner of L-Drago. As he and Gingka battle, Gingka is determined to win L-Drago back, but his anger, purposely provoked by Ryuga, stops him from winning, and as a result, loses devastatingly.

After losing to Ryuga, Gingka was in a state where he might even lose his passion for the bay. Kenta, unable to bear the sight of Gingka's state of mind, expressed his desire to help Gingka as a friend. Gingka was so moved by Kenta's words that he began to tell Kenta about his own past. It was a memory of a happy time in his home village. There he met his father, Ryūsei, the lord of Pegasis, whom Gingka respected the most. However, the peaceful days were shattered by Ryuga and Daidōji. They appeared to take L-Drago, which was sealed in the mountain.

Gingka has run away, possibly to his home town. Kenta, Madoka, Kyoya and Benkei follow him but after many calamities part ways. Then a strange man appears and saves Kenta and Madoka.

The man's name is Hyoma, whom Kyoya has his doubts about. Hyoma says he'll guide them to Koma Village, but Kyoya proves he's walking him in circles. Then Hyoma reveals a secret, and the fact he's an old friend of Gingka's. Meanwhile Gingka, en route to Koma Village, meets an old friend.

The gang arrive in Koma Village and are greeted by a talking dog called Hokuto. Hokuto tells them Gingka is climbing Mt. Hagane, seeking a scroll written by an old bearer of Pegasus. But then Gingka learns who the old bearer was and learns a valuable lesson.

Gingka takes friends to the bey forest where they are immediately excited. Meanwhile Hyoma, who is already jealous of Gingka's friends, challenges Gingka at a stadium called the Green Hades and reveals that as Gingka's true rival has never lost to Gingka in all their childhood.

Returning from Koma Village, Benkei and Kenta are furious with Madoka when she experiments with their beys without telling them. But then they learn how to switch parts, and that comes in handy at the Aquatic Tag-Team Tournament they've just entered.

The survival battle has begun, the winner being granted one wish. Everyone is entering, even Hyoma, Hikaru and Madoka. But despite everyone's enthusiasm there is a mysterious blader who has been defeating all his opponents...

Kenta and Benkei are aided by a new battler, Yu Tendo and his bey Flame Libra. Kyoya, after not finishing his battle with Hikaru, challenges Hyoma, who has been watching everyone but not battling. Kyoya wins, but at a price. Meanwhile Yu is upset the tournament is drawing to an end, and is challenged by Kenta, Benkei and Hikaru all at once. But as the battle goes on, Yu reveals himself to be the one who has knocked many of the 1000 competitors out of the competition with ease, and refuses to be taken down.

Gingka, Kyoya, Yu and Madoka are the final four left in the survival battle. Kyoya, after being aided by Madoka, drops out leaving Gingka and Yu left to battle. They both launch their special moves, but in the end, Yu is victorious.

As winner of the survival battle, Yu is granted his wish to hold a tournament to decide the strongest blader in the country. Then he reveals he's a member of the Dark Nebula, before leaving with Doji and Ryuga who showed up to taunt Gingka. After all agreeing to try to earn the 50,000 points needed to qualify for Battle Bladers, Gingka and his friends meet up at a stadium outside town to battle one last time.

As Gingka travels the country with Pegasus, he is challenged by many point hunters. He is saved by a mysterious blader, Tsubasa Otori, and his bey Earth Eagle. As they are entering the same tournament, the two bladers hang out together, Tsubasa giving Gingka some beyblade tips along the way. But as the tournament progresses, Gingka learns Tsubasa is hiding more secrets than he expected.

Kyoya is tired of the weak battles he is forced to battle in, until he learns of a strong blader nearby: Tobio, nicknamed Captain Capri, and his bey Storm Capricorn.

The Dark Nebula get a shock as Tsubasa, whom they have been watching, appears at their headquarters demanding to join. Doji agrees, but only if Tsubasa can pass a series of tests.

Kenta and Hyoma meet up at a duel tournament, Kenta battling in the forest stadium and Hyoma in the river stadium. But Hyoma is interrupted when Yu intrudes, demanding to battle. Then Kenta, who has already won his tournament, is challenged by Tsubasa. However, both Kenta and Hyoma are defeated by their opponents.

The fiendish Tetsuya follows Yu back to the Dark Nebula Headquarters. Doji though makes use of this and upgrades Tetsuya's bey as an experiment to Dark Gasher. At a tournament, Tetsuya defeats Benkei by cheating but loses to Gingka.

Kenta, whilst competing in a tournament, meets Sora, an impatient battler with amazing skills. Sora claims to be Gingka's apprentice with his bey Cyber Pegasus and attempts to copy Pegasus' special move, but cannot pull it off. At another tournament, Sora creates his own move, Avalanche Boost, but still loses the tournament to Kenta.

Gingka and the gang meet up at a tournament. But there is a mysterious atmosphere in one corner of the stadium as a mysterious blader Ryutaro tells fortunes... Gingka battles Ryutaro and creates a new move to defeat him and his Thermal Pisces.

Four matches are going on in the tournament. As Hikaru and Kyoya's match begins, the others, who were busy congratulating Gingka, realize they're last and in their haste bump into Yu. Then Tsubasa turns up and Yu explains they're both part of the Dark Nebula. Despite the others' shock, Tsubasa leaves barely saying a word, ordering Yu to follow him away. Kyouya wins his match against Hikaru as Tsubasa wins his against Benkei. Kenta takes on the twins: Dan and Reiki, that Kyoya faced at Dark Nebula's original base with their new bey Evil Gemios. They are on the verge of winning when the two start bickering and Kenta defeats them. Finally Yu wins his battle, but spends most of the time complaining about how only Tsubasa and Kenta appear to have good opponents.

The final six bladers of the tournament are: Gingka, Kenta, Kyoya, Yu, Tsubasa and Hyoma. Doji suggests they all battle against each other in a battle royal, mainly to see how well Tsubasa and Yu will get on batting together. Unfortunately, their hating of each other gets in the way and after taking out Hyoma, mainly by accident so they could get to Gingka, they start fighting each other. Pegasus plunders into the battle and all three lose. Finally Kyoya, who protected Sagittario whilst Yu and Tsubasa battled, defeats Kenta with a single hit and wins the tournament.

After the tournament, all the friends part ways. The Dark Nebula members head back to base, Yu though is still furious with Tsubasa. But without warning, the sneaky Tetsuya steals Gingka's point counter. It's rescued by a new and mysterious blader: Phoenix, who only agrees to give it back if Gingka can defeat him in a battle. Gingka loses to Phoenix, and Phoenix crushes his pointer.

Starting at square one, Gingka enters a tournament where he's challenged by a fan of his: Teru. Teru is a former dancer who suffered from an injury during one of his performances. When he was in hospital, he entertained himself by watching Gingka's battles. After a friend gave his Virgo, he has vowed to become a blader as strong as Gingka.

Ryuga has set out to obtain the 50,000 points to gain entry to Battle Bladers. He takes part in a 100 bey battle Benkei is entering and wins with ease and also beats Tobio and Ryutaro in the finals of a tournament he interrupted. Tsubasa and Yu, who have finally stopped bickering, are supposed to be guarding him, but Tsubasa gets fed up and leaves whilst Yu heads back to base to cause trouble for him. Falling into a trap set by Doji, Tsubasa sees his chance to swipe information from the Dark Nebula database. Though just as he is leaving, he is intercepted by Doji and many bladers Yu summoned to help out. Then Ryuga turns up...

Tsubasa almost loses to Ryuga but Eagle is saved by the sudden arrival of Phoenix. Taking pity on the young blader, Phoenix grabs Tsubasa and the two escape. Yu is at first really annoyed, but then explains to Doji he has already sent a Dark Nebula member to keep an eye on Gingka. Tobio interrupts a tournament where Gingka has entered where the stadium has moving walls. Tobio had an early advantage, but in the end Gingka triumphs with his special move.

Kenta arrives in a town where the kids are forbidden to battle in their stadium as it has been overrun by Busujima and a gang of bladers. Then Kenta's friend Sora turns up and they begin secret training to beat Busujima. Then one of their number vanishes and it's up to Sora to win her back. Sora battles Busujima, who creates a fire in the stadium. Gingka appears and puts out the fire with Storm Bringer and tells Sora to finish it. Sora calls on a new special move, O.V. Drive, and Cyber Pegasus knocks Rock Scorpio out of the stadium. The town has their stadium back and Sora celebrates with his idol Gingka.

Everyone has gained 50,000 points apart from Gingka, who is only 3,000 off. After learning of a nearby tournament, they all head there but are intercepted by Tsubasa. The others send Gingka on ahead whilst they distract Tsubasa, but this turns out to be what he wants. After Phoenix saved him, Tsubasa vowed to defeat Ryuga, but he was told to get to know Gingka's friends first. Kenta is willing to sacrifice everything for Gingka, but then the latter turns up, claiming he couldn't leave his friends behind. Tsuabsa becomes confused, but then Phoenix appears...

After Tsubasa is easily defeated by Phoenix, Gingka is also challenged. The rules are simple: if he wins he gets his lost points back, if he loses he is forced to quit beyblade. Everyone comes to show support for Gingka, even Kyoya. Finally Tsubasa understands what Phoenix had tried to tell him.

Battler Bladers has begun and everyone is winning their battles with ease. Benkei defeats Tobio and Kenta defeats Tetsuya. But Gingka's first opponent is Yu, the only person besides Ryuga and Phoenix who has ever defeated him. In the end, Gingka defeats Yu.

Hyoma's next opponent is Reiji, a blader who believes in fear and sadness being an important matter in bey battling. The others become worried about Hikaru's match against Ryuga that puts her in a coma.

Yu and Ryutaro learn of the horrors of the Dark Nebula as Ryutaro watches as his defeated friends are taken down by Ryuga. Yu is forced to battle Reiji, he almost loses, and Libra becomes badly damaged. Meanwhile, Tsubasa considers taking Ryuga on himself in order to stop Kyoya from having to battle him, but Kyoya stops him.

After a switch in the pairings, Kyoya is now battling Benkei, much to Tsubasa's delight as he now is battling Ryuga. Kyoya wins his battle but Benkei is pleased to have shown his old master his true strength. Meanwhile Gingka battles Ryutaro who, after watching the other Dark Nebula members fall at the hands of Ryuga, knows he is battling for his life. Ryutaro predicts a dark future for the world at the mercy of L-Drago, but after Gingka wins his prediction changes and he accepts his fate. After the battle, an injured Yu stumbles in looking for Kenta and Gingka.

Yu explains what has been happening within the Dark Nebula Organization, showing his broken Libra as proof. Gingka is furious, but not so much as Kenta who, after swapping performance tips, storms off to find and battle Reiji. The battle is intense, but Reiji defeats Kenta by breaking the claws off of Sagittario's Spin Track.

After Kenta and Yu's battle of will, everyone is looking for Tsubasa who has gone missing. He eventually shows up for his battle after some backup from Kyoya. The odds are stacked against Tsubasa, but after battling Ryuga once before, is there a chance he could win? However, Tsubasa loses to Ryuga who infects Tsubasa with L-Drago's Dark Power, causing the Dark Eagle events in Metal Masters.

Gingka prepares to battle Reiji who is stronger than in his first two battles. Meanwhile, Yu is kidnapped, and Kenta and Hyoma, who have both recovered from their battles with Reiji, race into the Dark Nebula Organization's HQ to get him back.

Gingka finally defeats Reiji, avenging the losses of Hyoma and Kenta. Phoenix appears to protect Kenta and Hyoma, beating Doji. Madoka tells Gingka about Yu, Kenta and Hyoma and the two rush after them. All of them regroup as shards fall from the ceiling, trapping Doji and shattering Phoenix's mask.

Phoenix, who is really Ryo Hagane, helps to rescue Yu. Then he explains to everyone about why he hid his identity, starting with the origin of beys, starting with Pegasus and L-Drago. Meanwhile, Doji comes across Ryuga who is anxious for more power and knows where to get it. He therefore takes all of Doji's power and stores it in L-Drago.

Kyoya finally gets to battle Ryuga, determined to avenge Tsubasa who had become a close friend. After persuading Ryuga not to use his special move, it really looked like Kyoya could win. But L-Drago had appeared to take too much battering from Leone, adding to its already brimming power, pouring it into Ryuga as the dragon spirits physically enter his body, mutating him partially into a dragon-like monster. Kyoya tries to hold his ground, but in the end he devastatingly loses, in a massive turn of events, and suffers the same fate as Hikaru and Tsubasa.

Upset at the fate of his friends, Gingka goes alone to the final battle. Ryuga battles him on a stage in the air, where Gingka struggles at first to defeat Ryuga, with his two special moves blocked by the latter. As L-Drago siphons the power from Pegasus and into Ryuga (with Ryuga laughing loudly and evilly), Gingka's friends come to help, giving him more strength for beating back Ryuga. However, as Gingka is ready to complete the "final retaliation," L-Drago again pours all its power into Ryuga, mutating him partially into a dragon, nothing like himself, but more masculine, and with glowing red eyes without pupils, and two purple trickles of fumes from his mouth, as well as a ripped vest, no cape, pointier nose, pointy teeth, many popping out veins, darker hair, and his voice combined with L-Drago's, showing that Ryuga was not himself.

Ryuga is first completely agonized and tries to fight L-Drago from conquering him, fading in and out and trying to talk. In the end he gets more pained and agonized as he collapses forward with a big explosion, jolting back with each of the dragons entering and re-entering him, then lunging forwards again after each one, screaming in agony, as Gingka and his friends watch in muted horror. Ryo then appears and explains to Gingka's friends that since L-Drago didn't belong to any one person in the first place, it consumed and destroyed that person since its power was too much for that one person alone, as is visible when Ryuga violently struggles with headache caused by L-Drago. L-Drago then manipulates Ryuga's mind once more, bringing him to L-Drago's senses, syncing him with his bey, and then rampages, laughing out purple dark energy, sending Gingka flying for its sheer amusement. Despite Gingka's initial efforts to fight the situation, Hyoma tells him that the one standing there isn't Ryuga any longer, which 'L-Drago' delights in, trying to absorb Gingka as sustainance. However, when L-Drago tries to destroy Gingka himself, Gingka is protected by the spirits of Kyoya, Hikaru, and Tsubasa, forming a wall. They tell him to use his Blader's Spirit and protect theirs. Finally, he realizes he can win with his greatest special move - Galaxy Nova, as well as his friends' and his own Blader's Spirit. This fractures L-Drago, and is so powerful that both Bladers lose their balance and fall to the ground from 500 feet up. Gingka is rescued by his bey Pegasus, and they rescue Ryuga, back to his normal self, as the Dark Power drained out of him during freefall. But, Pegasus disappears soon after landing, having over-exerted itself in the battle. Ryo reassures him that Pegasus will return again, and will spread its wings once more.