Yoshimori Sumimura, a 14-year-old junior high school boy, is a Kekkaishi, an exterminator of monsters. He is vying with Tokine Yumikura to be the heir to the Sumimura clan. Tokine is older than he, and she is his childhood friend as well as his rival Kekkaishi. To save people from danger, and to make himself stronger, Yoshimori fights against monsters.
Yoshimori feels quite crowded when Masamori and the Night Troops move into the neighborhood. He is further surprised to see that his older brother, Masamori, has ordered a few of his troops to assist the Kekkaishi of Karasumori.
It is now Kokuboro's turn to research the mysteries of Karasumori. Lead by the mysterious Hekian, with an ability called Thousand Eyes, a group of ayakashi, including Gagin's second in command Sakon, seek to find out the legitimate master of Karasumori. Yoshimori and Tokine try to regain some normalcy in their day to day lives.
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.
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.
Tokiko Yukimura has finally returned, just to announce that she will soon be leaving again. Masamori has managed to rebel against the wants of Ogi Ichirou, one of the heads of the Shadow Orginization, by deciding to movie the headquarters of his Night Troop. After Yoshimori hears of Tokiko's return he is bent on finding out about the passage to Kokuboro. After an amusing chase he is delivered a blow when he finds out that he is not strong enough to enter the Netherworld.
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.
As the castle begins to fall apart, Masamori and his night troops head into Kokubouro with the path created by Tokiko. Yoshimori rescued Sen and tells him to go back home while he still can. Wanting to be of some use to Yoshimori, Sen offers to help locate Kaguro. With Sen's help, Yoshimori speeds off to find Kaguro leaving Sen behind. Tokine manages to find the whereabouts of Yoshimori with Sen's information and heads off to Yoshimori with the intention of bringing him back to Karasumori before the castle completely collapses.
Old stories show that the passing of Gen Shishio has not gone unnoticed. The after math has shaken quite a few people, even some that would hesitate to call him a friend. Yoshimori and Masamori's makes a visit to the Shishio residence where that are met with disdain. Meanwhile the ranks of Kokuboro took a hit from Gagin's death.
Taking Tokiko's words to heart Yoshimori decides to put aside everything to be able to train. With a few words with a shrine priest Yoshimori takes some time to train with a few local crows. After Yoshimori decides that he has done well, he has a chance to put his new found strengths to the test when Karasumori is invaded by quite a few shady characters.
Yoshimori leads the trio, Sen and his friends, into a forest where he engages a friendly battle with them. Yoshimori easily overpowers Sen's two friends, but Sen manages to sneak right behind Yoshimori. However, at that moment a purple aura surrounds Yoshimori causing Sen to back away. Toshimori plays shougi with Masamori. Masamori finds Yoshimori in his special training ground and informs him that Kaguro is not someone he can deal with and that his goal should be to protect Karasumori. Meanwhile, Sakon prepares for an assault on Karasumori.
Tokine manages to infiltrate Kokubouro by following Shion. Masamori frees Atora and destroys Sakon with ease. As his night troops recuperate, he discovers that both Yoshimori and Sen are missing and that they are both currently in Kokubouro. Yoshimori is restrained by Shion's webs, but his aura repels anything else Shion tries to do to him. Byaku arrives and tries to plant a bug inside Yoshimori, but, he too, was repelled by Yoshimori's aura. Masamori gathers any movable night troops to head to Kokubouro. Matsudo Heisuke, along with his companion Kagami, busts through the ceiling, scares Shion away, and frees Yoshimori under agreement in which Yoshimori must not touch this "white" target. Heisuke and Kagami destroy the castle buildings while Yoshimori heads off to find Kaguro.
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.
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.
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.
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.
Tokine gets through the main entrance of Kokubouro, destroys Koshu, and continues her search for Yoshimori. As he is finding his way in the castle, Yoshimori sees Kaguro and stops only to contemplate about his current duties. He decides that his revenge will have to wait because his most important mission as of now is to locate and save Sen. While aimlessly searching the castle, he encounters the princess, who, unbeknownst to Yoshimori, gives him the map of the castle in his mind. After this encounter, the princess disappears and Yoshimori realizes that he, for some reason, knows his way in the castle now. He calls this his "natural intuition". Yoshimori saves Sen. Meanwhile, Heisuke found Byaku, who appears to be the "white" target that he was searching for to settle a score.
Heisuke, along with Kagumi, corners Byaku. It is revealed that Kagumi was Byaku's dead wife and that Byaku, though no apparent, is actually nine years older than Heisuke. Several flashback scenes occur as Byaku and Heisuke chat and fight (Kagumi does all the fighting for Heisuke). Byaku performed experiments on his wife and in the end she died. This traumatized Heisuke in the past because he loved Kagumi. The Kagumi with Heisuke now is actually a demon he made a pact with. Kagumi deals a crushing blow to Byaku's chest and disables in on the ground. Heisuke walks up to Byaku and asks if he ever loved Kagumi. Upon hearing "I have never loved anyone" from a disabled Byaku, Heisuke uses his cane to end Byaku's life.
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.
Yoshimori gets sick after desperately trying to erase an Ayakashi. That night, an Ayakashi with strange powers comes to Karasumori, but will Tokine and Shishio be okay without yoshimori?
Masamori gets promoted to seat 7 of the mysterious council of twelve, the elite leaders of the Urakai, but he needs to prove what he's worth. While at home, Karasumori and Yoshimori tries to help a dead cat pass on.
Aihi rescues Tokine who was about to fall into the depths of the castle. Aihi takes Tokine into her lab and Aihi's past was revealed. Appearently, Aihi lacks the evil aura that most Ayakashi has because she fell in love with a human. Shortly after Tokine leaves, Kaguro appears in front of Aihi and the two of them engage in battle. Kaguro easily defeats Aihi despite Aihi being a high class Ayakashi. Kaguro says the reason for her defeat was because she became weak from losing her desire to eat humans, but Aihi claims that Kaguro is also weak because he is insecure. In the exact moment where Kaguro is about to destroy Aihi, he senses Yoshimori's presence and heads off to him. Aihi transforms into her plant form and releases her dandelions; one of which makes its way back to the human she loved who is now an old man.
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.
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.
Tokine is finally reunited with Yoshimori in Kurosusuki, 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.
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.