| ShortSummary | - Yuichi is starting to remember more about his past encounters with Ayu seven years ago, and the time he gave her a present, which he will grant three wishes for her. At school, Yuichi finally discovers that Shiori's surname is the same as one of his classmate's, Kaori Misaka; he suspects they are siblings, though Kaori denies such a claim. As the dance festival starts without a hitch, it is not long before a demon comes to attack.
- As Akiko lies in the intensive care unit, Nayuki becomes deeply depressed. Locking herself in her bedroom, she refuses to leave. When she accidentally leaves her door unlocked, Yuichi uses the opportunity to talk with her, but she simply pushes him away. As Yuichi attempts to sleep it off, he dreams and discovers what happened to Ayu seven years ago. He leaves during a snow storm and heads for the woods, but soon collapses, and Makoto appears. When she kneels down to Yuichi's unconscious body, a bright light suddenly shines at them.
- Makoto starts her job working at a local nursery, and while walking home with Yuichi, they find a small, stray kitten, which is very affectionate towards Makoto. While talking on a bridge, Makoto drops the cat onto oncoming traffic, but it manages to survive. Yuichi gets angry at Makoto for this which causes Makoto to temporarily run away from home.
- At first, Mai makes a good impression at the ball, but the lights are destroyed and Mai is again implicated. When Mai faces expulsion, Sayuri convinces the student council to reverse the punishment by agreeing to join the council. On Mai's birthday, Sayuri is injured by the monsters Mai hunts.
- Today is Yuichi's first day at the local high school, and is admitted into Nayuki's class. As Yuichi is walking home to buy food for dinner, he runs into Ayu Tsukimiya, the girl from the day before, in the exact same situation. As they are walking home, they run into a quiet first-year student. When he goes to shop for groceries, a mysterious girl attacks him, but is exhausted from hunger.
- Shiori's birthday is days away and Yuichi wants to throw her a birthday party at a local café. He invites many students and classmates from school, along with Nayuki, Ayu, and even attempts to invite Kaori, who is reluctant to attend. As the minutes count down to midnight on her birthday, Yuichi and Shiori spend what could be their last moments together.
- It is now spring, and Mai and Sayuri have graduated. Although Akiko is on the road to recovery, a rift still remains between Nayuki and Yuichi. On the day Yuichi is scheduled to leave and transfer to another school, Nayuki sees a familiar name tag at the hospital.
- Makoto falls ill, and Yuichi discovers her true identity.
- Yuichi learns about Shiori's condition and Kaori's silence. Prompted by Nayuki, Yuichi spends an entire day with Shiori, forging happy memories.
- After his second day of classes, Makoto Sawatari tracks Yuichi down in the shopping district, trying to pick a fight. She collapses from hunger, however, and Akiko takes her in. The next day, after discovering some of her pranks, Yuichi suspects her of stealing his wallet.
- A miracle occurs and everyone is healed of her illness or injury: Mai, Sayuri and Shiori return to school, while Akiko comes home. In a startling discovery, Akiko reveals to Yuichi on the events after Ayu's accident and Yuichi finally finds her, lying comatose in the hospital. As time goes on, everyone moves on with their lives, but Yuichi still clings to the hope that she will eventually wake up. However, he is still missing a final piece of his puzzle, before Ayu can truly end living in a dream. In the end, Ayu wakes up and is still together with Yuichi. Just before the closing credits, a familiar fox can be seen walking just beyond the stump, slightly blurred into the background.
- Yuichi starts to spend more and more time with Makoto, and they become closer. However, a girl named Mishio Amano gives him an ominous warning about Makoto, and Yuichi's memories begin to resurface about her true identity.
- Yuichi searches for Makoto at night, and finds her in the shopping district. Shadowing her, he follows her to the hill overlooking the city and discovers that she found a stray cat. He takes both of them home, and the cat is named Piroshiki. Yuichi and Sayuri convince Mai to take part in the upcoming ball. Piro and Akiko fall ill, and Makoto and Ayu take care of them.
- Keeping his promise to Shiori, Yuichi offers to take her around town for the day to some of Shiori's favorite places. During the night, Shiori's older sister Kaori meets with Yuichi, explaining why she denies her sibling relationship, and the mystery behind Shiori's illness.
- As Yuichi and Ayu grow closer, Nayuki feels that she is being neglected by him. Ayu finally leads Yuichi to where her "school" is in the woods, but all they find is a large clearing with a tree stump in the center. The realization is too much for Ayu, and the unexpected happens right before Yuichi — she disappears.
- Yuichi reminisces about events of the past seven years ago concerning his first meeting with Ayu. Nayuki makes Yuichi return to school to retrieve her school notes she borrowed to him, and as he is leaving the premises, he runs into a third-year student, Mai Kawasumi, who is wielding a sword.
- Makoto's strength starts deteriorating as Yuichi finally remembers everything about her. Her condition worsening, Yuichi begins skipping classes to spend more time with her, hoping to buy her more time.
- Ayu still has not come back, and Yuichi continues to search for her and her lost item. In the meantime, Nayuki tries to cheer Yuichi up while trying to jog his memory about what happened between them seven years ago. However, Akiko becomes the victim of a car accident, which could lead to devastating results.
- Mai resolves to end the fighting once and for all. As Mai and Yuichi fight the monsters together, Yuichi traces another fragment of his lost memory.
- After what happened at the dance, the student council president Kuze attempts to get Mai expelled, and Yuichi tries to get her out of the situation. At the same time, Yuichi is not content with just standing by and watching Mai fight the demons alone and decides to help her anyway he can.
- Mai is called to the school's office, under the suspicion that she has broken one of the school's windows. Yuichi concludes that if Mai were more popular, she would not get into trouble as often, and invites her to the upcoming dance festival. Ayu makes an appearance and is offered to stay in the Minase household.
- Bringing the girl that attacked him home, Yuichi finds out she has amnesia and it quickly becomes apparent that the only thing she is able to remember is that she has a grudge against him. Despite Yuichi wanting to hand her over to the police, Akiko lets the girl stay, and as she begins to stay longer, she recalls her name: Makoto Sawatari. At school, Yuichi sees the same first-year student from the day before standing in the courtyard; she introduces herself as Shiori.
- The annual track meet tournament has come up, and Nayuki competes to win along with the rest of her teammates. A few days later, Yuichi again helps Ayu to try to find what she has been searching for, but they still cannot find it. Their time together in this endeavor brings the two of them closer than ever.
- Sayuri is starting to get more worried about Mai and Yuichi, which causes Mai to try to drive her away in order to protect her. On Mai's birthday, Sayuri meets with Yuichi in town and tells more about her family situation before she met Mai. Later that night, Sayuri goes to school to surprise Mai, but while there Sayuri is suddenly ambushed by the creatures roaming the school grounds.
- Yuichi and Ayu watch a movie together, and as they become closer, Nayuki is heartbroken. Ayu takes Yuichi to her school, but they make a startling discovery.
- Mai is implicated by the student council for some broken windows. Yuichi visits Mai again at night, but Makoto attracts the attention of the night watch. Makoto runs away from Akiko's house after a heated quarrel with Yuichi.
- Makoto's story finally comes to a resolution, while she spends her last moments bonding with her "family", and having all her wishes come true. Yuichi brings her to the place where she once belonged and performs a deep and personal ceremony for the two of them.
- With Shiori's birthday coming, Yuichi decides that he will try to do as much as he can for her, while she still has time. A week before her birthday, Shiori gets permission from her doctor to attend school for the remaining week, just like a regular student. Meanwhile, Kaori still insists on avoiding her, and warns Yuichi that Shiori might not survive long after her birthday passes.
- Yuichi wants Makoto to get a job in order to become more of a social person who has more common sense. On the same day as her interview, Yuichi goes out with Ayu to watch a scary movie, even though Ayu is completely terrified of horror films.
- Yuichi and Mai continue to battle the monsters, and when Yuichi is attacked, he is shown something he should not have forgotten years ago: memories between him and Mai who has a mysterious power.
- Yuichi runs into Mai and her friend, Sayuri Kurata, who invites him to eat lunch with them. When Makoto goes to buy food for Akiko, she uses the money to buy volumes of manga and nikuman. While Yuichi wants to scold Makoto to make her learn her lesson, Akiko simply decides to give Makoto her own allowance.
- Yuichi remembers what happened to Ayu, seven years ago, as well as the thing she was searching for—a little angel doll. Nayuki, Kaori, and Jun help him unearth the doll. Akiko is hit by a car in a blizzard. Ayu, in order to let Yuichi use the doll, asks him to let her go as a final wish.
- Waking up in an apartment, Yuichi meets an old acquaintance who he admired as a child named Makoto Sawatari. Back at their promised place, Yuichi sees Ayu again, and she asks for her third and final wish to be for Yuichi to forget about her, but Yuichi is unwilling to grant it. Ayu then makes a different wish, and disappears soon after in Yuichi's arms. Nayuki comes out of her depression, and she attempts to get her cousin out of his own.
- Yuichi attends his first day at his new school, and later meets Shiori Misaka after another run-in with Ayu. The next day he finds Shiori visiting the schoolyard.
- Yuichi finds Mai Kawasumi in battle at night in the school building. Following an incident at lunch with a stray dog the next day, he joins her for lunch. After school, he joins Ayu in her search for a precious object, with no results. That night, he brings Mai some dinner.
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