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. Following an incident that occurred five years ago, Yoshimori vows to protect Tokine from ever getting hurt.

During the day, Yoshimori and Tokine are normal students living a regular school life. At night, they protect the Karasumori site as Kekkaishi. One day, the Ayakashi Tsuchigama invades into the Karasumori school grounds. Yoshimori must run through the Tsuchigama's rain of attacks in order to destroy the Ayakashi.

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. Yomi reveals herself to be an enemy and explains her goal of taking over the Karasumori site in order to strengthen her demon, Yoki. Imprisoned, Yoshimori and Tokine find themselves in danger!

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. Yomi is then taken into custody for defying orders. As she departs, Yomi learns from Yoshimori the true meaning of kindness.

This episode begins where the last ended with the Kekkaishi cleaning up the mess created by Yomi and Yoki at karasumori. Shigemori explains to Yoshimori that within the Urakai is a group of users called the Yagyou who are an operations squad of the Urakai, and that the leader of the Yagyou is Yoshimori's older brother, Masamori. The episode continues to follow the story of Yoshimori's dealings with a ghost that is having trouble passing on.

Yurina Kanda, one of Yoshimori's classmates, is a girl who can see ghosts and spirits. To see one of the 77 wonders of Karasumori Academy - the unseasonable blooming of cherry blossoms - Yurina sneaks into the school grounds late at night. There, she witnesses Yoshimori and Tokine in the midst of exterminating the Ayakashi.

Masahiko, the ghost of a patissier, cannot pass on because he is worried about leaving behind his younger brother Toshihiko. Yoshimori meets with Toshihiko and tells him about his older brother, but is not taken seriously. To help the two brothers, Yoshimori decides to bake the same cake from the brothers' childhood memories.

Yoshimori trains a lot and tries to best Tokine as usual. His grandpa, Shigemori, mentally remarks how much power Yoshimori has. Yoshimori at the end breaks a boulder... and the garden.

A handsome teacher shows up secretly attacking students. Yoshimori is suspicious of the guy when he sees Tokine happily walking next to the guy and thinks about warning her of him being a possible dangerous player. At night, they sense an abnormality inside the school and they discover it is the teacher with three snakes wrapped around him. The teacher is actually a person with special powers but they still sense an ayakashi. It turns out that he was possessed by a parasitic ayakashi and they destroy it. The teacher is distraught that he attacked a student and is really nice by nature although he is still slightly perverted.

Yoshimori as a cake lover is obsessed with the legendary chocolate cake that his dad mentioned to him that is offered secretly to only 7 people at 5 AM at a specific cake shop. In order to hold a place in line, Yoshimori sends his shikigami but he is tired out and can't focus when fighting an ayakashi at Karasumori. Tokine worries about him but when she finds out the reason she becomes angry. Yoshimori then discovers that Shigemori ate his share of the chocolate cake much to his dismay. The next day Tokine reluctantly calls Yoshimori for help to kill a cockroach. Yoshimori manages to do so after Tokine accidentally pushes him on the ground smashing it. Afterwards, Tokine continuously avoids him but eventually gives him a thank-you gift: a T-shirt and the legendary chocolate cake.

It's another night of Kekkaishi duty. Yoshimori encounters three minor ayakashi, Honetarou, Uhosuke, and Nagao, and easily captures them. However, Madarao's old companion, Kouya, shows up and in anger attacks everyone, including his followers. After a brief flashback of Ginro (Madarao) and Kouya's happy past gone wrong at the hands of the humans, Kouya gains power from Karasumori and transforms. Yoshimori releases the seal on Madarao revealing his real form. Madarao and Kouya then battle.

After a long battle, Madarao is weakened and begins to accept death believing that Kouya will die as well but Kouya gains even more power from Karasumori. Just as Madarao is about to give up, Yoshimori steps in and tells Madarao that his master is not allowing him to die and thus Madarao stands up. The two work together and strike Kouya down. The dying Kouya tells Madarao to kill him but Madarao can't because he has no power left, but Kouya refuses to die at the hands of a human and so Karasumori lends its power to Madarao, finishing off Kouya. But before the group can celebrate, Madarao's true ayakashi nature reveals itself and starts attacking Yoshimori. But Yoshimori, with the help of Hakubi and Tokine, successfully seals Madarao once again through much difficulty.

Yoshimori thinks about being the legitimate successor and gets in a bad mood when he doesn't understand why he is the successor and not his brother, Masamori, who is more skilled than he is. At Karasumori, Yoshimori and Tokine encounter an ayakashi that stinks so bad that Hakubi and Madarao's sense of smell is greatly disrupted. Masamori watches from afar and is able to find the ayakashi with his partner, Kurohime, but sits back and watches how Yoshimori handles it. The ayakashi's shell is very hard and difficult to break and just before its blades were going to slice Yoshimori, Masamori interrupts its attack and destroys one of its blades. He then creates a 5 layer kekkai surrounding the ayakashi and destroys it. Masamori reveals to everyone that he will staying for a few days, much to Yoshimori and Madarao's unhappiness.

Yoshimori is really annoyed with Masamori being back especially when he thinks about how Tokine paid more attention to Masamori even in their childhood than to him. At night, Yoshimori and Tokine go to Karasumori and are confused when they can't find the ayakashi but then all of a sudden a forest grows and envelopes the school grounds. Madarao mentally notes that plant-type ayakashi cannot move and so someone must have planted it there. Masamori watches from afar and it is revealed that he was the one who planted it. Using the backdraft phenomenon suggested by Yoshimori, the two are able to destroy the ayakashi, although they had a huge mess to clean up afterward.

Yoshimori and Tokine called for help cleaning up and Masamori, Tokiko, and Shigemori show up. Yoshimori is annoyed the next day after being lectured for being reckless and gets even more so after thinking of the past. Later Yoshimori confronts Masamori about why he is watching him from afar. He then tells him that he wants to destroy Karasumori. After the conversation, Masamori uses Kurohime to search for anomalies. The next day, Masamori says to Shigemori that Yoshimori is above him. The family says farewell to Masamori as he leaves once again. Yoshimori asks Masamori to go bury Kouya's fur on his home mountain. Yoshimori promises to himself that he will surpass Masamori.

A strange god shows up at school in broad daylight. Yoshimori later finds out that it is Uro-sama who was looking for a kekkaishi who can fix his bed. Shigemori reveals that in the past he went to go fix the bed 50 years ago although Tokine says that Tokiko went to go fix it 50 years ago as well. The next day Shigemori and Yoshimori travel to the Colorless Swamp. Uro-sama opens up a portal to a different dimension in the swamp and Yoshimori jumps in.

Yoshimori is in a god's dimension and finds Uro-sama's bed to be a giant ball covered with vines and trees. He jumps inside and sees a box and restores it resulting in the plants to be blown away from it and the bed to be even bigger than before. Uro-sama becomes happy and jumps into the orb which causes Yoshimori to feel abnormal and rejected by everything in the dimension. He perseveres and tries to ask Uro-sama about Karasumori before the god falls asleep. After a while he is at his limit and is thrown out of the orb and dimension by Mamezo.

It's just a typical day for Toshimori but Shuji and Shigemori won't be home for the whole day and so he is stuck with Yoshimori. At school, Toshimori's friends get in trouble for not doing their homework and beg him to tutor them at his house. Toshimori is reluctant but eventually relents but also makes up a story about Yoshimori being very frightening. However, when they arrive home, Yoshimori greets them while wearing his baking attire. Later, Tokine visits bringing some dinner cooked by her mother but she encounters a cockroach and spills all the food on Yoshimori and the boys.

An elite team of Kokubouro comes to Karasumori during the day to ask for a negotiation with the Kekkaishi at night. However, the Ayakashi can't be trusted and the negotiations go wrong.

Yoshimori found a way to get out of the magical square, and is facing four Ayakashis. Yoshimori thinks of a plan to erase them but when his plan goes bad, Tokine gets taken as a hostage. Meanwhile, Shishio, who is almost lost in his anger, is fighting the 5th Ayakashi who seems to be just playing.

Shishio is troubled by his past but he will not tell the story to Yoshimori and Tokine. So, Yoshimori has no other choice than to ask his brother, Masamori.

Masamori entrusted Yoshimori, who wants to help Shishio with the tale of Shishio's past. Yoshimori is troubled with what to do and even Tokine can't help him, so he goes for a direct approach

Yoshimori, Tokine and Shishio are tested by the demon-tamer of the Yagyou squad, who also happens to be the mentor of Shishio.

Yoshimori, Tokine and Shishio are fighting in Karasumori while Kokubouro takes action against Matsudo Heisuke, the scientist that was helping Shige-Jii, trying to figure out what human skin are the Ayakashi wearing

Shishio receives an egg from Kaguro, an Ayakashi working for Kokubouro. When the egg gets closer to hatching, it is telling troublesome things to Shishio to confuse him.

While Shishio's egg is confusing him more and more, Kokuboro makes preparations for a full scale war. A large Ayakashi attack on Karasumori is coming, and it's coming fast

As Kokubouro descends, Masamori and his Night Troops are still preoccupied elsewhere leaving only Yoshimori, Tokine and Shishio to defend Karasamori. They end up in a battle with one of the leaders of Kokuboro. They must try their hardest to survive as all possible reinforcements are being distracted, and delayed by other Kokuboro forces.

The fight continues with Yoshimori, Tokine and Shishio fending off a hot headed Gagin. The only chance for relief is for Shishio to transform into his full form, breaking the taboo once again. Though the Kokuboro army is forced to retreat, the Karasumori gang gets delivered a devastating blow.