Shintaro, a young shut-in, has been spending his days in a funk in his apartment with Ene, an electronic girl who has taken up residence in his PC. When they go to a department store to buy a replacement for a broken keyboard, they find themselves taken hostage by terrorists. And that is when Shintaro encounters some mysterious people...

Momo Kisaragi, an idol and high school girl, was on her way to school for remedial summer classes. She is unable to make any headway as planned due to so many people coming up and talking to her, but being the center of attention and “drawing their eyes” is an everyday occurrence for her. What is not, however, is her encounter with a pair of unusual people.

After fleeing from the crowd, Momo encounters some people who know her secret. These people, who call themselves the Mekakushi-Dan (Blindfold Gang), encourage Momo to join their group. Momo decides to join up, and then the group visits a department store, the very same one that Momo's older brother, Shintaro, had gone to with such grim resolve.

After getting caught up in the chase with Momo, the young boy, Hibiya Amamiya, spends time with his friend, Hiyori Asahina, who he has a crush on. However, his plans to spend the summer with Hiyori is hindered by both her cold attitude towards him and her smitten behaviour towards the strange resident, Konoha. The following day, on August 15, Hibiya finds himself in what appears to be a dream in which Hiyori is hit by a truck whilst chasing after a cat, whispering something before she is hit. As this dream seems to loop, Hibiya attempts to keep Hiyori from danger, but she is always killed in some manner upon encountering a black cat. In the end, Hibiya decides to take Hiyori's place as the victim by throwing himself in front of the oncoming truck, mocking the cat before he is hit.

Shintarō awakens at the Mekakushi-Dan's hideout, finding himself in an awkward situation when he is caught in his underwear trying to get Ene to tell him where he is. After the situation eventually dies down, Shintarō is informed that he and Ene have been made members of the Mekakushi-Dan, much to his dismay. As the others decide to go to visit the grave of the founder and former commander of the Mekakushi-Dan, who committed suicide two years ago, Shintarō storms off elsewhere, where he ends up encountering Konoha, who is searching for Hibiya and Hiyori, and gets roped into helping him. When they spot the two children being dragged into a van by some mysterious people, Konoha rushes in to rescue them, displaying superhuman strength, but soon a truck comes skidding towards them. Meanwhile, as the others arrive at the commander's grave, where Kido shows a picture of the commander, Ene recognises her as a girl named Ayano Tateyama.

Prior to the start of the series. Takane Enomoto and Haruka Kokonose are both classmates tasked by Kenjirō with creating a special project for their school culture festival, deciding to go with a shooting video game. During the festival, Shūya (Kano) brings Tsubomi (Kido) to Takane's booth to play the game Kenjirō designed, with Tsubomi showing exceptional skill in the game whilst Takane finds her experience mysteriously hampered, which Shūya later reveals was cheating on Tsubomi's part. Later, Takane tries to hide from people interested in playing against her due to her ranking 2nd in a gaming tournament, but Haruka gives her the confidence to face them. However, she becomes shocked when Shintarō comes by the booth and completely defeats her. Afterwards, Takane is introduced to Kenjirō's daughter, Ayano, who reveals she and Shintarō will become her schoolmates, and the group get to know each other over the following year. On August 15th, during summer classes, Takane decides to ignore Haruka as he sleeps, unaware that he is actually in pain.

After discovering Haruka had become hospitalized after collapsing, Takane runs into Ayano at school, who tells her she needs to be more courageous and tell Haruka what she needs to tell him, leading her to realise that she loves him. Moments later however, she falls unconscious herself, and dies. She then says her last words, "Haruka, I love you." After coming in contact with a mysterious void, she eventually awakens as Ene. Back in the present, as Ene finishes explaining her situation, Kano reveals that her situation is a lot like what the other Mekakushi-Dan members went through. Just then, Seto calls informing the gang about the traffic incident Shintarō became involved in. While Momo, Kido, and Marry go to check on him, Ene stays behind with Kano to ask him for more details, not wanting Shintarō to hear anything, since he doesn't know Ene and Takane are the same person, only to learn that Haruka had also died alongside Ayano. In a flashback, it is revealed that Haruka's desire to have a strong body led to a peculiar situation of his own: Konoha.

After Momo's group catches up with him at the hospital, Shintarō tries to explain his situation as best he can. After running into Hibiya, who seems aware that the incident was no accident, Shintarō tries to get some information out of him, but he suddenly collapses. Kido, realising that Hibiya is manifesting a power of his own, has him taken back to the hideout to recover. As Seto goes off to search for Kano, Kido explains to Shintarō and Momo how each of the Mekakushi-Dan's members gained their powers after escaping from a mysterious rift, called the "Heat-Haze", which appears during near-death experiences, with Momo gaining her powers after nearly drowning, losing her father in the rift in the process. Hibiya, who had overheard that Hiyori is trapped in the rift, runs off in search for her. While Kido and Momo chase after him, Shintarō discovers a photo of Ayano whilst checking up on Marry.

The episode looks back as Ayano and her family takes in Tsubomi (Kido), Kōsuke (Seto), and Shūya (Kano), helping them to control their powers. Ayano acted like a big sister to her companions, staying strong even after her mother was lost in a landslide. One day, Ayano discovered some notes written by mother, researching an old folk tale that appears to hold the origin of the children's powers. Later on, following the school festival, Ayano realised from reading her mother's notes that Kenjirō also possessed powers of his own, an alleged 'snake' that had its own will, asking Shūya to help her investigate. Back in the present, Kano, who had been explaining the story to Ene, explains that the king 'snake' is trying to bring together all the other 'snakes' in this world, before leading her to a secret laboratory inside a school where Ene's real body, Takane, is being kept.

A past event is shown where a woman named Azami is attacked by men believing her to be a monster, but she fights back using her powers in order to protect her daughter, Shion Kozakura. After learning from the remaining survivor about how her husband, Tsukihiko, got hurt trying to defend her, Azami makes the painful decision to leave her family behind in order to protect them from any further harm. As time went by, Shion eventually gave birth to Marry and raised her by herself, making sure she wouldn't leave her home. One day, when Marry steps outside, she is caught by a pair of thieves, and although Shion uses her powers to stop one of the thieves, she is weakened, as a result and they are both killed by the second thief. As both Marry and Shion are dragged into the same realm as Azami, ruled over by a large snake, as a result of dying on August 15, Azami uses the last of her strength to pass on her role to Marry, allowing her to return to the real world. Some time later, Kōsuke hears Marry's internal cries with his own power and comes across her, deciding to become friends with her. Back in the present, Marry comes across Konoha on the street and takes him back to the hideout, deciding to become friends with him and take him to where the others are.

Shintarō wakes up and recalls a tragedy that he had seen over and over in his dreams, awakening to a power he always had, before taking a pair of scissors to his throat. Meanwhile, Momo and Kido catch up to Hibiya and offer to help him search for Hiyori, but are suddenly surrounded by a group of people. Elsewhere, Kano recalls how Ayano, who rejected the idea of sacrificing the other snake-wielders in order to grant her father's desire to see her mother again, confronted the snake possessing Kenjirō before committing suicide and becoming swallowed by the Heat Haze in order to prevent him achieving all the snakes needed. Despite Ayano's sacrifice, the snake refused to relinquish Kenjirō, stating his plans to start from scratch by using Takane and Haruka's bodies. Back in the present, as Momo and the others are imprisoned by their kidnappers, Momo uses her powers to attract all the Mekakushi-Dan's members, including Ene, who had returned to her original body, to their location. Meanwhile, in an unknown location, Shintarō reunites with Ayano.

Kano informs the group of the situation as they make their escape, using their powers to get past all of the guards. When the group end up getting lost, Hibiya uses his power of clairvoyance to pinpoint Kenjirō's location and soon arrive in his lab. The snake claims that the current world was created by Marry due to her wish to be with her friends, resulting in a endless loop of the snake being revived. The snake then possesses Konoha's body, using its immense power to overwhelm Kido, Kano, and Seto, coercing Marry to take their snakes and try to begin the cycle all over again. However, the words of her friends keeps Marry from going through with it. At the moment, Shintarō and Ayano arrive and, with assistance from a previous world's Konoha, give Marry the power to swallow everything. Believing in the future over a fantasy world, Marry overcomes the snake, who is destroyed by Konoha, before having a brief reunion with her mother. The series ends with Shintarō and Ayano in the real world and reuniting with the others.