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.

When an ogre-user and member of the Urakai named Yomi who knew Tokine's father arrives in town, Tokine is forced to remember her fathers death. Even though the Urakai have been introduced as being on the side of "good" Yomi is strangely suspicious, and not completely trusted.

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.

Because of the power of Karasumori a huge cherry tree blossoms in front of the school completely out of season. The tree attracts curious students as well as power hungry Ayakashi.

This episode continues where the last left off with the spirit of a pastry chef that refuses to pass on. Yoshimori helps him throughout the episode to fulfill his dying wish so he can pass on in peace.

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 ayakashi disguised as a human sends three ayakashi to Karasumori and has then run around the place before allowing them to run amok in order to gather information. Yoshimori attacks one of them and it becomes angry and the observer eventually gives the signal. They gather together but Tokine destroys one of them making the other two angry. They combine and are empowered by Karasumori. Eventually Yoshimori and Tokine destroy the ayakashi and they send for clean-up help. But Madarao and Hakubi notice the human scent changing into an ayakashi scent and Yoshimori jumps to the roof to investigate finding the spy.

Yoshimori engages in battle with the spy but the spy runs away. Yoshimori chases after him outside the school grounds but the spy runs into the forest. Yoshimori envelopes a large part of the forest with a kekkai and the spy is trapped, but then he drinks a power-up drink and strengthens himself and rips the kekkai apart. The spy swings his arm in a circle creating a mystery circle and uses the confusion to escape. Yoshimori is left with the spy's right arm as evidence.

A new transfer student shows up and destroys a shiki disguised as Yoshimori. Yoshimori senses it and wakes up from his nap on the roof and tries to find Gen. Tokine and Yoshimori find claw marks on the wall outside along with the remains of Yoshimori's shiki. Gen encounters Tatsumi and senses that he has special powers. He begins to interrogate him but then leaves him alone. Later at night, Tokine and Yoshimori met Gen at Karasumori.

Yoshimori and Tokine find out that the transfer student, Gen Shishio, is a member of Masamori's Night Troop and was in fact sent by Masamori to protect the Kekkaishi of Karasumori. Meanwhile gramps is doing some research on the "skin" that the Ayakashi dropped.

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Yurina discovers that her friend Aoi has developed a crush on Gen. Together with her friends, they try to get Gen to realize her feelings.

A very popular boy comes to meet Tokine in school. When Yoshimori sees them leaving, he follows them together with Gen, who is suspicious of the boy.