While in Zawame's Free Performance Zone, Mai and Mitsuzane of the dance team Team Gaim are having a free-spirited dance when members of rival Team Baron scare them away when an Inves Game gets out of hand. When Mai goes to former teammate Kouta Kazuraba to reveal something strange has happened, he reveals that Team Gaim's leader Yuya gave him a strange Lockseed, and Mai reveals Yuuya informed her of it as well. The two eventually find a way into the Helheim Forest that has appeared in the Free Performance Zone.

Kouta tries to use his new abilities to help out at his part-time job, but he only gets in the way. And when Yuuya mysteriously disappears, Kouta wonders if what happened in the forest was real, and now that he is in charge of Team Gaim, he must lead the group in a dance-off against Team Baron.

Kouta starts to gain a reputation in Inves Games by fighting them as Kamen Rider Gaim, when Kaito Kumon reveals he too has a Sengoku Driver and the Banana Lockseed.

Kouta and Kaito work together to try to find Yuya, but they instead face off against an even more terrible enemy.

Kouta tries to overcome the events that befell him in the Helheim Forest against Zangetsu while Kaito challenges Mitsuzane to a fight, with the new Armored Rider Ryugen unable to fight Baron on his own.

Hase and Jonouchi transform into Armored Riders Kurokage and Gridon, but something strange happens during their fight with Baron against Gaim and Ryugen. Later, Kouta tries to get a part-time job at a pastry shop, only to be disturbed by the effeminate head chef.

After easily defeating both Kurokage and Gridon, Kamen Rider Bravo steals their Lockseeds and sets his sights on defeating all of the Armored Riders. Kouta is angered that Oren has made it his mission to defeat all of the Armored Riders, but Kaito just tells him to beat him to get it over with. Before long, Bravo issues a challenge to Baron, but it is not Baron who he is really after.

After his defeat at the hands of Bravo, Kaito believes he is no longer strong enough and seeks out a new strength. While Kouta seeks out a new job, Mai finds herself trapped in the Helheim Forest again, forcing Kouta and Mitch to go and rescue her.

Kouta and Mitsuzane must hunt down a fully manifested Inves that is randomly attacking people in the city while also dealing with keeping up their Beat Rider ranking.

As the Lockseed gathering "game" begins, Baron and Bravo fight between themselves, while the white Armored Rider, Kamen Rider Zangetsu, investigates the infiltration into Helheim Forest. Meanwhile, Kouta, who has also entered the forest, decides to track down the white Rider and finds the base of operations that may be the cause for the tears into Helheim Forest opening on their own.

Kouta and Mitsuzane attempt to warn the Beat Riders about Yggdrasill's manipulation, only to find that Yggdrasill is deploying Kurokage Troopers to silence anyone who knows the truth as Zangetsu uses a new belt model. Meanwhile, Mai encounters the mysterious girl who resembles her.

A mysterious bacteria is infecting people in Zawame City. In the crisis situation, Kouta, Mai, and Mitsuzane try to find out the cause behind this.

After Hase transforms into an Inves, Gaim tries to take him out before he can do much damage but finds it difficult to harm someone who he believes is still human inside. Meanwhile, Baron does his best to combat Zangetsu Shin but is overcome by Kurokage Troopers and captured. And Mitsuzane, who realizes his brother is their foe the white Armored Rider, infiltrates the Yggdrasill Corporation headquarters on his own to see what is truly going on.

With Kouta and Kaito both captured by the Yggdrasill Corporation, they are brought to Ryoma Sengoku who reveals that he created the Sengoku Drivers and Genesis Drivers, and reveals the truth about the Helheim Forest to them. Elsewhere, Mai and Zack try to convince the other teams to hold off the Inves Games due to the damage they cause and how they are missing most of the Team Leaders. While under Yggdrasill's custody, Kouta is approached by DJ Sagara who tells him more of the truth behind the Yggdrasill Corporation, and suggests that he do something about it.

After escaping the clutches of the Yggdrasill Corporation, Kouta wonders why all three of them were able to escape so easily, knowing how Ryoma Sengoku was interested in them. Later, Mai and Chucky continue to try to convince other teams to end the Inves Game, but they instead witness an Elementary Inves robbing a jewelry store. Meanwhile, Takatora has shown Mitsuzane a horrible scene hidden within the Helheim Forest and revealed that he easily beat Kouta.

After Takatora reveals the truth about Helheim Forest to Mitsuzane, he tasks his brother with recovering Kouta's Sengoku Driver. Elsewhere, Oren and Jonouchi plan to perform the same act with their own plan in mind. Kouta later receives a phone call that tells him his sister has been kidnapped.

Mai tries to host a dance contest to bring everyone's morale up, but none of the teams will participate. Mai tries to get Kouta to convince Team Baron to join, but he is not sure that he will dance either. It is only the appearance of Oren who changes the minds of the others, as he turns their friendly dance competition into an outright fight.

Duke fights against Gaim and Baron and manages to come out on top. As they lick their wounds, DJ Sagara appears and gives Kouta a present in the form of a Tulip Hopper Lockseed. When they arrive in the Helheim Forest, they are quickly surrounded by Yggdrasill, pressuring the two Beat Riders to fight to stay alive.

Takatora shows Kouta the truth behind Helheim Forest, at the same time Kaito would learn the same thing from Ryoma, Sid, and Yoko. Meanwhile in Zawame City, more Inves invade and it's up to Mitsuzane and Zack to stop them.

The Helheim Forest will soon destroy the Earth if no one acts on it. Kouta informs Mitsuzane about this fact and says they must do something, but Mitsuzane is hesitant as he already knows the truth. Meanwhile, Kaito examines a photograph taken from within the Helheim Forest and believes he sees a human figure, then goes into the forest to investigate.

The Crack at Yggdrasill's lab causes more and more Cracks to appear throughout Zawame. Kouta believes the solution is to close Yggdrasill's Crack before any more Inves can attack. However, Kouta encounters Ryoma and Yoko waiting for him in Helheim Forest, ready to stop him so their plans may continue.

Now aware that he killed Yuya, Kouta loses all will to fight, and will not even seek to destroy the Scalar System. As he struggles with the thought of telling the truth to his friends, Kaito encounters the strange Inves in Helheim Forest, once more.

Baron continues to attempt to defeat the Over Lord Inves to no success, until Marika suggests a new plan. Mitsuzane tries to get Kouta, now that he has the Peach Energy Lockseed, to track down the Over Lord Inves, while also finding out that DJ Sagara has been helping him all this time, leading him to wonder who Sagara really is and what his plans are.

After watching Kouta, Mitsuzane, and Zack battle Inves, Jonouchi realizes that the dance team days are over, again. Later, Oren arrives to begin Jonouchi's next set of training. Kaito tries to tell Kouta about the Over Lords, while DJ Sagara is confronted by Ryoma, Yoko, and Sid. After Gaim, Bravo and Gridon fought the Inves that appeared Oren and Jonouichi goes home but Jonouichi reveals to Oren that the Inves Game is no more. Later, Oren finds a crack and tries to investigate it but discovers something yet to be revealed.

Mai wants to know why Kouta has been hiding from her, and he reveals the truth to her about Helheim Forest, as well as the Inves and the fate of Yuya, upsetting Mitsuzane, who is still under orders from his brother. Meanwhile, Kaito plans to finish his fight with Demushu.

Kouta is knocked unconscious by Ryugen's backhanded attack, and Baron fights Ryugen for acting so cowardly. Meanwhile, Takatora mulls over the idea of having to cull the Earth's population down to only one billion people through the use of the Sengoku Drivers, remembering back to the days of first developing them, unaware that even then Ryoma was conspiring against him. When Kouta regains consciousness, he explores Helheim Forest once more, only to be approached by someone unexpected.

Takatora reports to Ryoma, Sid, and Yoko that Kouta will be working for them in hunting down the Over Lords in an attempt to stop Helheim Forest. They agree to the plan, but the next time they all enter Helheim Forest, Ryoma has set up a trap to take Takatora out of the equation.

In the forest, Takatora is saved by the Over Lords and introduced to their leader Rosyuo who tells him of their past as the Femshinmu people and the secrets of Helheim. Later, Kouta, Kaito, and Mitsuzane all search the forest for Sid, but Sid has set a trap for Kouta. Then Kouta fights with Zangetsu Shin in Helheim Forest, unaware that it is actually Mitsuzane attacking him using his brother's weapons.

Kouta and Mai meet a young man who can remember nothing about himself other than his name, Jiro. During a rain storm, Kota tries to pull Jiro out of the rain, but noticed his hand feels like metal instead of skin, bringing up the question if Jiro is a robot. Elsewhere, Ryoma looks over the schematics for an android developed by a colleague. Its model name is Hakaider.

The "Fruit of Knowledge" gives someone the power to remake the world itself and become God. Sid overhears from one of the Over Lords, Redyue, that Rosyuo has been safeguarding the fruit. Sid plans to steal it so he can become God. While this unfolds, the Over Lord Demushu has left Helheim to invade Zawame City and begins to randomly destroy the city.

Baron Lemon Energy Arms and Knuckle cannot hold off Demushu forever, and he escapes them. With Sid murdered at the hands of Rosyuo, he instructs Redyue to continue the invasion of Zawame much to Takatora's shock and terror, while Mitsuzane seeks out the Fruit of Wisdom still. Elsewhere, Kouta wakes up, and DJ Sagara presents him with something that will help him out.

The Inves are invading, Kouta's sister takes shelter, and Kouta patrols with the others. Trying to get the Golden Fruit, Ryoma reveals Project Ark to the world, which erupts into chaos. Then, without help from the Japanese government or Yggdrasill, Kouta and the other Riders lend a hand to the people left behind.

With the world falling into chaos thanks to Ryoma, Zawame City has become an isolated place infested with Inves. Kouta's sister Akira, along with others in shelters, go outside to call for help. Meanwhile, Redyue broadcasts an announcement over the radio to the whole world stating that Helheim will completely take over the Earth in a year. At the same time, Inves are commanded to hunt the citizens of Zawame City. Yoko confronts Mitsuzane about his actions as Zangetsu Shin and whether or not he will tell Kouta, while Redyue plans on using human technology to further her own goals as well as bring back Rosyuo's queen. But to do that, Redyue requires a sacrifice.

Rosyuo begins the invasion of the Earth by opening Cracks around the world. Kouta, Kaito, and Yoko plan an assault on the Yggdrasill tower to stop him, while Kouta also seeks out Akira. However, Mitsuzane has other plans after seeing Mai, again.

As Mitsuzane/Zangetsu Shin is about to kill Kouta, Takatora appears and stops him, revealing the two's relationship as brothers to Kouta. Later, the fight of the two brothers begins as Takatora returns as Zangetsu to fight Mitsuzane.

Kaito meets DJ Sagara, who provokes him and summons a ghost-like Gaim Kiwami Arms. After the battle, he gets caught up in an alternate world where he leads Team Baron in the competition for soccer's All Rider Cup.

Mitsuzane seems to be hallucinating, claiming he can see Takatora even though he knows he defeated him. Elsewhere, Ryoma returns to Zawame City, and Kouta believes he may now be an ally against Mitsuzane and the Over Lords.

Kouta and Ryoma work together to break into Yggdrasill Tower to free Mai and Akira.

Kouta follows the passage to Yggdrasill Tower and to his surprise discovers an underground dungeon. Redyue informs Kouta that he has become one of the Over Lords, rather than a human, and proceeds to show him his apparent destiny.

Kaito fights with Mitsuzane but the two are disrupted by Ryoma. Meanwhile, Mai talks to Rosyuo and is entrusted with the Forbidden Fruit before entering a fight against Kouta and Kaito.

Kouta tries to prove that he has not changed, despite all Kaito has seen in Helheim, and helps the others clear Zawame of Inves. However, Mitsuzane and Ryoma discover that Mai, who has been taken ill, is now the host of the Golden Fruit, and wonders why Rosyuo has placed it in her.

As Gaim and Ryugen Yomi continue their battle, Kaito realizes that there is only one way for him to surpass Kouta now that he possesses the powers of the Over Lord King.

As Mai accepts the powers of the Golden Fruit and attempts to change the fate that has befallen her friends, Kaito seeks her out to gain its power, as well.

Zack sets a trap for Kaito, but... Meanwhile, Kouta has gained command over an Inves army whilst battling Kaito.

Betting both their lives and beliefs, the final battle between Kouta and Kaito reaches its conclusion.

Seven months after Kouta and Mai have left and colonized a new planet, all traces of Helheim Forest have been cleared from Zawame City, but a returning threat appears to change things forever. Mitsuzane realizes that Kouta isn't on Earth anymore and that it's up to them to save Zawame City.