The Kekkaishi's mission is to exterminate the Ayakashi that appear within the Karasumori site. As legitimate heirs, Yoshimori Sumimura and Tokine Yukimura carry out their family tradition as the Kekkaishi...

During the day, Yoshimori and Tokine are normal students living a regular school life. At night, they protect the Karasumori site as Kekkaishi...

Yomi Kasuga, a Demon Tamer, pays a visit to the Yukimura family under orders from the Shadow Organization. Her arrival causes Tokine to recall the painful memory of the day her father Tokio died...

The Karasumori's power causes Yoki to go out of control. Even Yomi is unable to stop her demon now. Hakudo and Odo, who were sent by the Shadow Organization to pursue Yomi, arrive and destroy Yoki...

Yoshimori meets a human ghost who used to be a patissier. The friendly ghost gives Yoshimori some tips on how to bake better sweets...

Hekian and others show up in the Colorless Swamp in an attempt to discover the secrets of the land of Karasumori. Yoshimori and Tokine learn about the mystery of the Demon Fox of the Black Pampas Grass from Mamezo. Realizing their importance to the survival of the Kokuboro realm, Byaku looks to the Kekkaishi for their power.

Masahiko, the ghost of a patissier, cannot pass on because he is worried about leaving behind his younger brother Toshihiko...

Yoshimori is gifted with enormous Kekkai power, while Tokine is skilled with precise control over creating the Kekkai. During the battle against the Ayakashi Hiwatari, the two combine their power and skill to defeat the enemy. Realizing each other's strength, both are determined to train even harder to polish their Kekkai techniques.

Yurina Kanda is still troubled by her spiritual powers and asks Yoshimori how to deal with being different from others. Meanwhile, Tatsumi Mino, the substitute English teacher, approaches Tokine. Realizing that Mino is under the control of a parasitic Ayakashi, Tokine and Yoshimori work together to save the teacher.

Yoshimori is depressed after being yelled at by Tokine. To help cheer up his son, Shuji tells him about a legendary chocolate cake. Yoshimori uses his shikigami to go buy the cake, but is discovered by Tokine. Fed up with Yoshimori's irresponsible actions, Tokine refuses to talk to him ever again. But the following day, a black monster appears in the Yukimura residence, forcing Tokine to ask for Yoshimori's help.

Madarao is reunited with Koya, an old acquaintance from Madarao's past. Long ago, the two dogs lived together in the mountains but were chased out by humans. Driven by his hatred for humans, Koya attacks Yoshimori. Madarao asks Yoshimori to undo his seal so that he can settle his score with Koya. Regaining his true form, Madarao begins his battle to the death!

With Yoshimori's help, Madarao succeeds in defeating Koya. Madarao delivers the finishing blow to his old friend Koya, as it was his last wish. But the Karasumori's power causes Madarao to go out of control. With help from Tokine and Hakubi, Yoshimori attempts to re-seal Madarao's power and return the demon dog back to his former self.

Masamori Sumimura, chief of the Night Troops, is the oldest son in the Sumimura family. Though gifted, Masamori was not born with the Hoin mark, creating a somewhat strained relationship with his younger brother Yoshimori. One night, Yoshimori and Tokine battle against Sasorigama. Unable to pierce through the Ayakashi's tough exterior, the two find themselves at odds when Masamori makes a surprise return to the Karasumori site.

Masamori gives Yoshimori a lecture on the application of the Kekkai and how he needs to think before he acts. That night, Masamori places a botanical Ayakashi in the Karasumori site to test both Yoshimori's skills as well as the Karasumori site's powers, only to learn both are beyond his expectations.

During his conversation with Masamori, Yoshimori declares that he intends to seal the Karasumori's power forever. Just then, a spy is sent from an unknown organization to observe the Karasumori site. Feeling its presence, Masamori goes after the intruder.

Lord Uro, a local deity and former resident of the Karasumori site, suddenly appears at Karasumori Academy. He requests Yoshimori to accompany him to the Colorless Swamp where he now lives to fix his 'bed.'

Yoshimori jumps into a black hole in the swamp only to arrive in a mysterious domain where he finds Lord Uro's bed. There, he uses the restoration technique on a magical device and successfully accomplishes his mission, but not before endangering himself by entering the divine field.

Toshimori's classmates come to the Sumimura residence only to run rampant around the house. Frustrated with their behavior, Toshimori instinctively uses his Kekkai, accidentally knocking them out. Depressed about what he has done to his friends, Toshimori is cheered up by Yoshimori, gaining a newfound respect towards his older brother.

The spy returns to the Karasumori site once again, this time accompanied by the Ayakashi triplets known as the Shirahago. Yoshimori and Tokine are having difficulty fighting the triplets' feather attacks, but manage to destroy one of them. But the remaining two use the power of Karasumori to merge and become a giant Ayakashi.

With the Karasumori's power, the Shirahago transforms into a much more powerful form. Using teamwork, Yoshimori and Tokine finally manage to destroy the Ayakashi. Gaining sufficient data about the Karasumori site and the Kekkaishi, the spy makes his escape, only to find himself being pursued by Yoshimori.

Yoshimori and the others are distressed to learn that Ayakashi are now able to blend in to society disguised as human beings. Meanwhile, Mr. Mino, a teacher with special talents, is attacked at Karasumori Academy in broad daylight. The perpetrator is Gen Shishio, a new transfer student also with special abilities, who was sent in by the Shadow Organization.

Yoshimori finds out that the person who assigned Gen to the Karasumori site was none other than his older brother Masamori...

Ohkubikuruma appears at Karasumori Academy, and during the battle Gen is injured...

Gen fights Gagin with his forbidden total transformation, but in the end, Kaguro takes Gen's life. The Kokuboro quickly retreats when the Princess's condition suddenly takes a turn for the worse, while Yoshimori and the others...

An Ayakashi by the name of No Otoko takes control of Kimiya Hachioji and abducts Tokine...

Having caught a cold, Yoshimori is unable to protect the Karasumori site as usual. An eager Shigemori takes over his grandson's duties...

Masamori is appointed to the seventh seat of the Council of Twelve, who are the top executives of the Shadow Organization. Meanwhile, the spirit of a black cat possesses Kurosu, Yoshimori's homeroom teacher...

A group of Ayakashi wearing human skin boldly breaks into Karasumori Academy in the middle of the day. That night, Yoshimori, Tokine and Gen begin negotiating with the intruders for the control of Karasumori. Their offer declined, Gen is immediately overcome by Kaguro's deadly blade, putting Yoshimori and Tokine in great danger.

Furious and helpless from the continuous attacks directed at him by Kaguro, Gen attempts to perform a complete transformation but is stopped by Hiba. Kaguro, fed up with his companions' performance, kills them and leaves Karasumori. Gen is relieved of his position as support personnel for the Kekkaishi for breaking his oath...

After being discharged from Karasumori for breaking his oath, Gen becomes more withdrawn than ever.Yoshimori resorts to approaching his older brother Masamori to request that the decision to dismiss Gen be rescinded. Masamori proceeds to tell Yoshimori about Gen's past...

Yoshimori hears about Gen's past, about how he was taken in by Masamori and his Night Troops after he caused a terrible incident four years ago. After a stern warning from Hiba, Gen is left to continue his assignment to protect Karasumori.

Atora, the person who was in charge of raising Gen, suddenly appears at Karasumori to test the teamwork of Yoshimori, Tokine and Gen. Realizing what's at stake, they try to work as a team, and eventually, their bond allows them to pass Atora's test.

Shion, a member of the Kokuboro, successfully assassinates Matsudo when he finds out their location in another dimension. Shigemori hurries to his rescue but arrives too late, though in reality...

Aihi advises Byaku to move the princess to the Karasumori site to regain her power. Meanwhile, Kaguro appears before Gen once again, and Yoshimori accidentally witnesses the meeting between them. Although Gen rejects Kaguro's offer, he is left conflicted due to Kaguro's egg, a 'gift' from him that continually beckons Gen to join the Kokuboro.

As Tokiko travels in search of the Kokuboro, the Night Troops, led by Masamori, head to the far reaches of Japan as ordered by Ogi. Seizing their chance, the Kokuboro conducts a full-scale attack on the lightly defended Karasumori!

As Shion attacks the Sumimura and Yukimura residences to stall Shigemori, Gagin of the Kokuboro shows his true power and overwhelms Yoshimori and the others. Having run out of options, Gen fights Gagin, undergoing his total transformation, which was strictly forbidden...

Gen fights Gagin with his forbidden total transformation, but in the end, Kaguro takes Gen's life. The Kokuboro quickly retreats when the Princess's condition suddenly takes a turn for the worse, while Yoshimori and the others...

Sen and the other Night Troop members cherish their memories of Gen at a memorial service held on the grounds of the Shadow Organization. Masamori and Yoshimori then attend Gen's family funeral where they meet his older sister, Ryo.

Hekian and others show up in the Colorless Swamp in an attempt to discover the secrets of the land of Karasumori. Yoshimori and Tokine learn about the mystery of the Demon Fox of the Black Pampas Grass from Mamezo. Realizing their importance to the survival of the Kokuboro realm, Byaku looks to the Kekkaishi for their power.

Tokiko returns home but soon leaves for the Black Pampas Grass once again. Yoshimori secretly follows Tokiko in order to avenge Gen but is quickly discovered and rebuffed, as she believes he still needs to learn how to use his powers properly.

To develop a more effective use of his powers, Yoshimori begins his training with a group of rambunctious crows living at a woodland temple. Using the advice given to him by Tokine and the temple monk, he finally perfects his method of making precise consecutive Kekkai attacks... but as he does, he finds himself surrounded by a mysterious group!

In order to defend Karasumori from the Kokuboro, the members of the Night Troops, led by Masamori, move into the Sumimura residence. Yoshimori meets with Atora to apologize for what happened to Gen, but...

Sen and his friends from the Night Troops decide to test Yoshimori's skill in a skirmish. Meanwhile, Tokine worries about the battles to come, as the Kokuboro attacks Karasumori once again.

While Masamori and his Night Troops mount a defense against the second coming of the Kokuboro, Yoshimori allows himself to be captured by Shion to be led back to Kaguro. Amidst the chaos, Tokine follows him, not knowing that Sen was captured as well.

Back at the Kokuboro, Yoshimori is threatened with the life of Sen unless he follows Byaku's orders, but he still refuses. As Yoshimori is slowly being tortured in order to bend his will to do the Kokuboro's bidding, Matsudo appears.

For the time being, Yoshimori chooses to rescue Sen rather than battle Kaguro. As he searches for Sen, he unknowingly meets with the Princess, who bestows upon him the power to find his way through the castle maze...

Byaku and Matsudo's grudge begins with the death of Byaku's wife Lisa. For fifty years, Matsudo had been looking for Byaku to fulfill a promise...

As the Kokuboro collapses, Yoshimori looks for Kaguro, only to realize that he has become separated from Sen. Sen, on the other hand, meets up with Tokine to look for Yoshimori, but...

Getting separated from Sen, Tokine runs into Aihi who does not attack her on sight. Instead, she shares her past about how long ago she enjoyed spending time with a human who was not afraid of her. Listening in on the conversation secretly and annoyed by her memories, Kaguro proceeds to attack Aihi, gravely wounding her in the process.

Tokine is finally reunited with Yoshimori in Kokuboro, but without any time to waste, Yoshimori immediately goes into battle to settle his revenge with Kaguro. During the fight, Kaguro finally reveals his past.

As the final showdown between Yoshimori and Kaguro continues, Sen enters the battle haphazardly to help Yoshimori. Sensing that Sen is in danger, Yoshimori instinctively unleashes his Zekkai. Although Kaguro is defeated, Yoshimori loses consciousness in the process, trapping both Sen and himself within his very own Zekkai. Although Masamori and the others arrive, they are left helpless. Running out of time, Tokine makes a rash decision.

Yoshimori is unconscious, and Tokine decides to jump into the Zekkai, effectively waking him up from his trance. With the help of Tokiko's power, Yoshimori and the others escape from the crumbling world of the Black Pampas Grass. At last, the Night Troops' mission has finally come to an end, and life at Karasumori returns to normal.