The story is a love story between Seimei and Yuki that started more than a thousand years ago. Through various re-incarnations, they've never been able to life happily ever after...

I've only played Koyuki's route, which given the story, is probably the most appropriate.

Primary Characters:
Makoto Kusanagi: Main character of the story. He belongs in the school drama club and is the playwriter for Asuka's play.
Koyuki Kusanagi: Main female character. She's actually Makoto's cousin, but calls him "brother" anyway. She just started at Makoto's high school.
Asuka Izumo: A mysterious new student who shows up and presents an old book that she wants them to perform.

Present Day:
It is summer break, but there are still a few students in the dorms including Makoto and his room mate Shin (name is actually Makoto also, but can be pronounced as Shin so they do that for distinction). One of Makoto's favorite places near the school is a place called the "Sealed Hill." He goes there and finds that his cousin, Koyuki is there. She informs him that she's going to be attending his school. They go to the drama room where she meets the other students of the club that have remained. They decide to do a play for the schools opening after break but don't know what to do. Then, Asuka walks in with an old book and says she wants it acted out. Makoto is put in charge of writing the script based on the book.

Act I, Heian Period:
Seimei (played by Makoto) is a mage during the Heian period who can summon up various creatures. As he rids some robbers, he stumbles onto a young girl (played by Koyuki). At first, he tries to scare her with his beasts, but it turns out that she's blind. She has no memories of who she is and where she's from. He takes her in and gives her the name "Yuki (Snow)." On his way back from a festival, they find Tamamo (played by Asuka) outside their door. He also takes her in. Later Seimei runs into Hidesato (played by a teacher) who he has been led to believe killed his father and has been seeking vengence ever since. Hidesato tries to explain to him that his father wanted to die (they were at war and didn't want to die from an enemy's wound) and he was the one who had to do the deed. Yuki also steps in and stops Seimei from killing him. After the incident Seimei explains to Yuki the situation. Seimei meets his mom, Kuzuha, some time later and she gives him a sword to use on Hidesato for killing her husband, but to use it, he has to kill Yuki who's apparently the keeper of the sword.

Present Day:
Nana, another student, doesn't seem to be able to play the part of Kuzuha's shikigami. But just their luck, another new student, Madoka, shows up. She's perfect for the part.

Act I, Heian Period Continued:
After a few more encounters with Kuzuha (through her shikigamis), Seimei and his mother get in a scuffle and Yuki gets killed while trying to stop them from fighting.

Present Day:
They formally invite Madoka into the group, Makoto prepares the second act, and more everyday life with the characters. Nothing too interesting.

Act II, Kamakura Period:
The second play happens during the Kamakura period and starts with Oohime (played by Koyuki) whose about to be wed to Yoshitaka Kiso (played by Makoto). Their wedding is more politically motivated than anything as her father is a lord as well as his father. She really doesn't want to be married off and just wants life to continue as it always has, with her doll "Tsuki (Moon)," and her two maids, Mikuri (played by Asuka) and Yae (played by Nana). When he comes to visit, she gives him the cold shoulder and despises him. However, when she drops her doll down a cliff and Yoshitaka goes to retrieve it, she starts to like him. Days later, he meets a monk (played by the teacher who played Hidesato) who comments on the sword that Yoshitaka carries around. He tells Yoshitaka to rid the sword as it's a bad omen. But as a samurai, he refuses to part with his sword that's been in his family for generations. He then finds out from Yae, who's playing a double agent for his dad, that his dad is planning to attack Oohime's father and wants Yoshitaka to kill Oohime. He refuses to do so. And runs away with Oohime when the army comes. He tells Oohime to run ahead and he'll meet up with her later. She gives him her doll, Tsuki as good luck. He then meets up with Oohime's mother who turns out to be the re-incarnate of Kuzuha and Tsuki was her brainchild to keep tabs on Oohime, who's Yuki re-incarnate. Yoshitaka then realizes that he's Seimei. The mom and son kill each other and again, Seimei and Yuki's love is broken. Oohime keeps on waiting for him to return, even when she knows he's dead.

Present Day:
Koyuki seems very bothered by the play, but Makoto doesn't seem to understand why. Asuka asks Makoto if he feels anything for Koyuki, but he's still clueless. At the "Sealed Hill," Sakura flowers suddenly start blooming.

Act III, Taisho Period:
The last act happens during the Taisho period with Shinichi and Seiji Nakamoto, a pair of male twins both (Makoto). They live in an apartment building with Asuka Kuze (played by Asuka) and Yukimi Asou (played by Koyuki). Yukimi is apparently the landlady, but she has a terminal disease so she has to stay quarantined in her outhouse. Asuka visits Yukimi often and tells her story about Seimei and Yoshitaka. Seiji also visits her and has fallen in love. Despite the fact that his brother is the novelist, he tries and starts writing down the stories that Asuka tells Yukimi about the people in the past. One night, he has a dream about a kimono girl and wakes up hearing a scream from the "Sealed Hill." The legendary sword has been unearth. Things then start becoming very strange as Seiji feels like Shinichi is acting a little different. Seiji also has more and more dreams of killings followed by actual slayings in his city. At the climax, it's revealed that Seimei has been re-incarnated as both Seiji and Shinichi, but that Yukimi, Yuki's re-incarnate loves Shinichi and Seiji's memories about her are all Shinichi's. He was also the one killing people (in his jealously, I suppose) and has now killed Yuki. When he realizes this, Seiji kills himself and waits for their next re-incarnation.

Present Day (Sakura):
Makoto finally realizes that he and Koyuki are Seimei and Yuki, Yoshitaka and Oohime, and Shinichi and Yukimi. Asuka and the teacher (both re-incarnates themselves, but knew it long before) find out that the sword, which was hidden in the "Sealed Hill" has been unearth and taken. They try to take Yuki away, but she comes back. Turns out that Madoka is possessed with Kuzuha's spirit and they have their showdown in the church where they rehearse. Makoto and Koyuki defeat her and Kuzuha gets re-united with her husbands spirit. On the day that school starts, Koyuki stops calling him "Onii-chan" and calls him a more appropriate (for lovers), "Makoto-san."