Riku Tachibana seems to be an ordinary middle school student with the worries of what club to join. His unique feature is that he makes odd hand gestures, and he does not know what they really are. His childhood friend Momo-chan goes through the first of many denials of liking Riku as more than just a friend. Riku decides to ask his grandfather what the gestures mean, and soon after, he finds himself making a contract with the Shikigami, Byakko no Kogenta.

The news of Yamase's disappearance has reached Chi-ryuu Toujinshi Ujiyama and Yuuma Asuka, who has just defeated a Toujinshi of the Ten-ryuu with his powerful Shikigami, Byakko no Rangetsu. Much to Ujiyama's dismay, he is told by Yuuma to investigate Yamase's leads on the Head of the Ten-ryuu. Meanwhile, as his grandpa rests in the hospital, Riku searches for clues on some old documents found in his grandpa's bedroom. However, it is not long till Ujiyama and his Shikigami, Oobi no Mumyou, confront Riku and Kogenta.

Following a lead from his grandpa's notes, Riku goes to Ooiwasai to search for some more In. Soon after, he is attacked by Misasa, a Chi-ryuu Toujinshi, and her Shikigami, Kanro no Komaki.

Following a lead from their new friend, Masaomi, Riku and Kogenta go to the mountain region of Myoureizan in search of the In for "Saikaidou Kotetsu." Along the way, Riku meets a Toujinshi of the Ten-ryuu, Teru. Because he doesn't want to get Riku involved, Teru goes off by himself. Soon after, Riku and Kogenta fight against two Chi-ryuu Toujinshi, Hazan (Shikigami - Enoki no Otochika) and Dougen (Shikigami - Tsubaki no Gorouza). Teru joins in the battle with his Shikigami, Akagane no Isoroku. Also, Riku finds out the identity of Kogenta's "partner.

One night, Masaomi explains to Riku about what Toujinshi and Shikigami are, and why the Ten-ryuu and the Chi-ryuu are currently fighting. It seems that the Chi-ryuu is interested in opening the Fukumaden Kimon, a gate that leads to demons and a power that could destroy the world, and the Ten-ryuu are trying to keep the Fukumaden Kimon closed. Masaomi also says that when Toujinshi lose their Shikigami, the Toujinshi lose their memories. Later, when Riku decides to clean up the damaged shrine, Yuuma confronts him, asking him about the Head of the Ten-ryuu. Then, his little brother, Souma, sick of Yuuma being on Mikazuchi's side, steps in and attempts to fight with him. However, Yuuma and Rangetsu end up fighting against Masaomi and his Shikigami, Seiryuu no Kibachiyo.

Kogenta really wants Riku to start training, but Riku doesn't know how to go about it. Then, thanks to some of Rina's books, Riku gets some information on a special area for training. So, he, Rina, and Momo find a training area for using Toujinfu (cards for Toujin seals). Before the training could actually begin, Riku and Kogenta must fight against another Earth Style Toujinshi, Gonpachi, and his Shikigami, Souka no Raiden. The battle gets tough when Riku and Kogenta have to deal with Gonpachi and Raiden and also have to protect Momo and Rina from the demons that reside in the training area.

The Boat Club goes on their first outdoor practice. Riku, though, has an objective to fulfill while on this trip. Using translations of his grandpa's notes, he and Kogenta find a new In. Meanwhile, Danjou, a Chi-ryuu Toujinshi, and his Shikigami, Akagane no Misohito, terrorize a nearby rural town in search for a Ten-ryuu Kimon and then open it. To do so, they force the village leader into showing them the location of the Kimon. Riku and Kogenta find and confront Danjou and Misohito. When Riku decides to use the newly-found In, it inexplicably doesn't work.

Souma gets frustrated by Mikazuchi, his brother Yuuma, and the Ten-ryuu. So, he decides to run away, but he doesn't have any money. With no place else to go, he heads back to Riku's destroyed shrine. There, he and his Shikigami, Ikazuchi no Fusanoshin, fight Kirihito, a Chi-ryuu Toujinshi, and his Shikigami, Uzumibi no Mingobee, who have been requested by Mikazuchi to eliminate Souma.

One night, Kogenta decides to teach Riku a new In as proof of their trust towards each other: Hissatsu - Hundred Ghost Obliteration Attack. As described by Kogenta, it focuses all of his remaining energy into one powerful blast. After the attack, however, Kogenta would be unable to move, and if the enemy survives, then Kogenta would be completely defenseless. Kogenta takes this matter lightly, but Riku thinks that he's just being selfish. Now, Riku tries to find ways to get stronger as a Toujinshi (while leaving his Drive with Kogenta stuck in it in his freezer). Soon after, Riku is challenged by Izou Kenzaki, a rank-5 Chi-ryuu Toujinshi, and his Shikigami, Kurogane no Fuji. Riku, with a more serious (and scary) look of determination on his face, and Kogenta fare well against Izou and Fuji. But when Izou starts to use cheating methods, Riku must choose whether or not to use the new In that Kogenta taught him.

Riku's grandpa finally wakes up, and he tells Riku to go to the Ten-ryuu Taihaku Shrine in Kyoto. He eventually finds the Taihaku shrine and meets a young girl who seems to be the only person working at the shrine. She begins Riku's "training," but then a Chi-ryuu Toujinshi named Chihaya busts in and summons his Shikigami, Kaede no Kurenai. When they are about to finish off Riku and Kogenta, the girl reveals herself as Nazuna, a Toujinshi of the Ten-ryuu, and summons her Shikigami, Hiiragi no Horin.

The Chi-ryuu learns that Chihaya has disappeared from his post at the Taihaku shrine. So, Mikazuchi sends Izou and two rookie Chi-ryuu Toujinshi, Shinonome (Shikigami - Hanmou no Ninkurou) and Kasumi (Shikigami - Mebuki no Fuurai), to Kyoto to investigate. Yuuma also comes to Kyoto for his own reasons. Teru finds his way to the Taihaku shrine, and shortly after, he starts his training. He also takes a liking to Nazuna-chan. It's not long until Izou, Shinonome, and Kasumi make it to the Taihaku shrine and fight with Riku, Nazuna, and Teru in a huge battle royale. As the fight goes on, Izou grows desperate and becomes willing to take out on of his own teammates in order to win.

While Masaomi and Kibachiyo fight Yakumo and (one of) his Shikigami, Seiryuu no Buryune, Riku and Kogenta battle Yuuma and Rangetsu. When all else fails, Riku decides to use the In that Kogenta taught him before: Hundred Ghost Obliteration Attack. But something strange happens to Kogenta after Riku uses it...

Kogenta is severely injured after the battle with Yuuma and Rangetsu. Nazuna uses a technique in which Horin heals Kogenta. Riku leaves the Taihaku Shrine with Momo and Rina to give Kogenta the time he needs to recover.

Riku gets a note from his grandpa that he has left on a journey. When Riku goes to the destroyed shrine, he finds the site completely rebuilt. Nazuna tells Riku about the moon magatama and how it can allow people to enter and exit the world of Fukumaden at shrines. When Souma tells them that the Earth Style has already been in and out of Fukumaden, Riku and Nazuna take it upon themselves to go into Fukumaden. They end up in a grassy moss field. They use their Onmyou divination board to help them navigate, only to find two Earth Style Toujinshi, Kanna (Shikigami - Shuusui no Erekiteru) and Mozu (Shikigami - Hiiragi no Toubee).

Mizuki wants to be recognized by her fiance, Yuuma, who's too busy tending to the battle-scarred Rangetsu. So, Mizuki teams up with Kanna to enter Fukumaden and find a Toujin stone. Nazuna goes back to Kyoto to bring back her belongings so that she can move into Riku's house. Souma wants to go to Fukumaden with Riku to show that he can be useful, despite Nazuna's words. The two groups meet and battle in a rocky mountain field. Souma and Fusanoshin get in an electrifying battle with Kanna and Erekiteru while Riku and Kogenta fight with Mizuki and her Shikigami, Kanro no Kuradayuu.

Mozu teams up with easy-going Kikusaki (Shikigami - Houjou no Ruri) to search for more Toujin stones, and a deranged Izou goes with them, hoping to destroy Riku and Kogenta. Teru meets up with Riku and Souma. They head into a desert field of Fukumaden, where they do battle with Mozu, Kikusaki, and Izou.

Momo, Rina, and Ryuuji come with Riku and Nazuna to a water field in the Fukumaden. Riku, Kogenta, Nazuna, and Horin then must fight underwater against the Chi-ryuu's Mutsuki (Shikigami - Gyoujaku no Ebihiko) and Daikan (Shikigami - Shuusui no Ryuukon).

Masaomi's bike gets a flat tire. A passerby on a motorcycle helps repair his wheel. As a way of showing his thanks, Masaomi gives the man a special coupon. It is revealed later that his name is Hayate Takamiya, a Toujinshi of the Chi-ryuu.

Riku recieves a letter from Teru. It says that he needs his help at the Kitaguni Hot Spring Village Shinzansou. It turns out that Teru ate a lot of food that wasn't his at an inn in Shinzansou. So, to pay off his debt, he's working for the inn. But the real reason why Teru requests Riku's aid is that he needs his help in getting rid of the demons that have been attacking the people of the inn.

Oosumi, the Technology Research Department Chief for the Chi-ryuu, speaks of putting a Toujin stone into a Shikigami. When the revenge-driven Izou hears about this, he takes the Toujin stone he got from a while back into Fukumaden with him. Riku, Souma, and Nazuna head into a rocky mountain field of Fukumaden in search of more Toujin stones. Riku gets seperated from the group, and he is soon confronted by Izou. They summon their Shikigami and do battle. Kogenta easily handles Fuji, but when Izou embeds his Toujin stone into his Shikigami, Fuji then transforms into his Daikoujin form and starts beating Kogenta.

Riku wakes up and finds himself in another part of Fukumaden. He is then attacked by a masked Toujinshi named Taishin and his Shikigami, Shousetsu no Magahoshi. They think that Riku is the Ten-ryuu Toujinshi named Yakumo. With Kogenta unconscious, all Riku can do is run away, using Toujinfu to help him escape. Outside the Fukumaden, Masaomi appears and learns of the news that Riku is gone. Masaomi, Nazuna, and Souma return to the rocky mountain sector of Fukumaden to search for Riku. They are soon confronted by Mizuki and Kanna. When Riku is cornered, the real Yakumo appears and summons Buryune to fight the masked Toujinshi and Magahoshi, who are actually a part of a faction called the Jin-ryuu.

Riku and Kogenta arrive in a tranquil part of the Fukumaden. Riku feels very nostalgic about this place. But a Chi-ryuu Toujinshi, Gaitatsu and his Shikigami, Aogane no Nanaya, come and decide to destroy the place in search of the Toujin stone.

Riku has been having a lot of dreams lately, each involving a pleasant yet sad woman. When the giant Kimon in the Mikazuchi building opens, a lot of Youkai run amuck. Although Mikazuchi closes the Kimon with ease, there are still some Youkai out there. So, Nazuna uses Toujinfu to gather the remaining Youkai, and then Souma and Fusanoshin finish them off. At night, Yuuma and Rangetsu return and fight Riku and Kogenta. Kogenta is winning the battle, but Riku seems to be in a daze.

Kogenta is dead, and Riku has lost all of his memories from when he was a Ten-ryuu Toujinshi. So, he doesn't remember Souma, Nazuna, or the boat club. Masaomi discovers that Riku's contract with Kogenta has not been cut. But, Riku seems to be rejecting his contract for some reason. To get Riku to accept his contract and restore his memories, not only will Kogenta have to be revived, but Riku will also have to walk down a difficult path, one that will reveal his ancient past.

Riku has regained his memories and is reunited with Kogenta. He also meets Yakumo again, who tells him about the Fukumaden and the past. There once was a man named Utsuho, and he had the terrible power to control the Youkai. He used the Youkai to attack Kyoto, the capital city at the time. The Toujinshi used their power to fight Utsuho and eventually won. Utsuho and the Youkai were sealed in a dimension far away. The Toujinshi split into two factions: the Ten-ryuu to guard the seal and the Chi-ryuu to destroy the Youkai that leaked out of the seal. The place where Utsuho is sealed is the Fukumaden. Soon after, the Jin-ryuu Toujinshi Taishin and his Shikigami, Magahoshi, return and attack the group. Riku runs away, and Yakumo chooses to fight him alone. With his new Zero Drive, Yakumo seems to be making short work of Taishin.

Riku and Souma head for the Chi-ryuu base, the main building of Mikazuchi Products. Along the way, Souma gives Riku some backrgound information on Mikazuchi, the Head of the Chi-ryuu. He has made a great impact on Japan with his projects and mergers. Mikazuchi is also an expert Toujinshi, and it is said that he uses the power his Shikigami to control his "luck" in the market. When they enter the building, Souma is left behind while Riku heads up to see Mikazuchi. Riku meets him and asks what was the crime that the Ten-ryuu committed a thousand years ago. Mikazuchi explains that the Ten-ryuu were not guarding the seal of the Fukumaden. Instead, they were taking provisions and resources from the Fukumaden. Thus, the Chi-ryuu had suffered many casualties from the Youkai that were coming out of the unguarded seal. So, the Chi-ryuu attacked the main Ten-ryuu base. Then, Riku and Kogenta fight Yuuma and Rangetsu once more atop of the building.