The battle rages on as Shirou continues to protect Sakura, now consumed by the darkness. He joins forces with Rin to end the Holy Grail War, while Illyasviel, who knows the truth behind it, confronts her fate. Amidst the chaos, Zouken plots to manipulate Sakura for his own desires. The final fight begins.

August 1995: Mikiya first meets Shiki in a white kimono during a snowing day. Later on, at the high school freshmen ceremony, Mikiya sees Shiki in the crowd and chases after her, introducing himself to her. But Shiki hides a big secret: A wave of bizarre murders occur around many loose ends, and no suspects. there are still many questions: Who to believe? Who is the murderer? What is the secret of Shiki? and especially: Who is SHIKI?

In a Holy Grail War, Mages (Masters) and their Heroic Spirits (Servants) fight for the control of the Holy Grail—an omnipotent wish-granting device said to fulfill any desire. Years have passed since the end of the Fifth Holy Grail War in Japan. Now, signs portend the emergence of a new Holy Grail in the western American city of Snowfield. Sure enough, Masters and Servants begin to gather... A missing Servant class... Impossible Servant summonings... A nation shrouded in secrecy... And a city created as a battleground. In the face of such irregularities, the Holy Grail War is twisted and driven into the depth of madness. Let the curtain rise on a masquerade of humans and heroes, made to dance upon the stage of a false Holy Grail.

Tomoe Enjou is attacked by bullies from his old school and saved by Shiki Ryougi. He asks her to hide him at her place and admits that he killed someone. Several days later, there are still no broadcasts about the murder as if it didn't happen... and when the victims are found, they're alive and unharmed.

June 1998: After spending two years in a coma caused by a traffic accident, Shiki Ryougi awakens with amnesia. She is visited by Touko Aozaki, a wizard and proprietor of a studio called Garan no Dou. Shiki has lost not only the memory of her accident, but also any real sense that she's even alive. Strangely, enigmatic beings begin to attack her...

The story starts following an incident: a young girl jumps from the top of a building. The image provokes a certain dread, as the girl appears to have been a corpse even before she jumped. The case is dismissed, yet more and more of these suicides occur, and all from the same building. Thus began the rumour, that a ghost inhabited the rooftop of the building.

Ten years after the Fourth Holy Grail War, a devastating clash between Masters and Servants, another war erupts. Shirou Emiya, whose father fought in the first battle, was leading a peaceful life with the warmhearted Sakura Matou. But when hidden forces begin to stir, Shirou resolves to fulfill his father’s dying wish, protect Sakura, and fight for the Holy Grail.

A side story of the original Kara no Kyōkai - the Garden of sinners movie series divided into 2 parts. In the first part, Shizune Seo, who finds her life too predictable due to her precognition, and Mitsuru‎ Kamekura, who uses his precognition to be a professional bomber, meet Mikiya and Shiki, respectively, and their futures begin to change. In the second part, 10 years after the original series, Shiki and Mikiya's daughter, Mana Ryōgi, spends a day with Mitsuru.

In February 1999, a string of murders has Shiki Ryougi and Mikiya Kokutou on edge. These crimes share a disturbing resemblance to a similar set of homicides from 1995, when Shiki and Mikiya first met, and awaken a dark, murderous desire that has laid dormant within Shiki's soul ever since then.

July 1998 - After a group of delinquents is found dead in their hangout place with all their limbs twisted and torn off, Aozaki Touko receives a request to find the murderer and asks Shiki for help. The main suspect is Asagami Fujino; a girl who was the boys' plaything until recently, who Shiki believes to be "one of her kind".

January 1999: Apprentice mage Azaka Kokutou, Mikiya's younger sister, has been ordered by her mentor, Touko Aozaki, to investigate a certain incident in which fairies steal the memories of students at Azaka's school, Reien Academy. Azaka launches an investigation with the help of Shiki.

Despite his adoptive father's warnings that the girl found in the remnants of a destroyed city is too dangerous to be considered anything other than a tool or weapon, Shirou Emiya comes to treat Miyu as a younger sister. But when Shirou relaxes his guard and Miyu starts normal school, the Ainsworth family and their agents swoop in, kidnapping the girl with the goal of sacrificing her! Faced with the realization that Miyu's ability to do good will always be equaled by her capacity for destruction, Shirou must attempt to both rescue his adopted sister, and decide how to confront the threat that her powers will always pose.

The world is dying, no longer able to support life. The Ainsworth family can use the Holy Grail to save humanity, but the price of salvation is sacrifice of the magical girl Miyu — but Miyu’s brother, Shirou, won’t let them have her without a fight. Now it’s up to Illya to step in and find a solution that will save not only Miyu, but the entire world for impending doom. But when the price for the world's salvation is the life of a single, innocent girl, what will Illya choose?

March 1999: Mikiya Kokutou meets Shiki Ryougi again at the same place where he met her for the first time four years ago...

Fate/Prototype is a reimagined version of Kinoko Nasu's original version of Fate/stay night. The storyline takes place eight years after the tragic Heaven's Feel. Here, the Holy Grail is still the so desired object. However, the darkness under this so-called "Grail" is revealed while the characters proceed to fight against each other in order to win.

Shirou has lost his Servant, Saber, and is no longer a Master in the Holy Grail War. Despite this, he refuses to leave the battle, determined to protect Sakura. Meanwhile, a mysterious shadow engulfs the city, killing Masters and Servants one by one. As Shirou faces new dangers, Sakura is drawn deeper into her own destiny as a mage.

The story follows three girls — Kaede Makidera, Kane Himuro, and Yukika Saegusa — at Homurahara Academy, but has nothing to do with the efforts to restore the Human Order.

Mikiya Kokutou gives Shiki Ryougi a cat to watch, as he will be away for a little while. Though Shiki protests, he leaves the cat anyway, and Shiki is stuck trying to understand her new feline companion. But as luck would have it, the cat seems to have taken a liking to Mikiya and misses him. Later in another part of the city, Ririsu Miyazuki visits the place where her dear friend committed suicide. She intends to end her life as well, but she meets Fujino Asagami, a blind classmate with a traumatic past. Though the two girls don't have much in common, Asagami reminds Miyazuki of her lost friend and helps her understand her pain. Two months later, Mikiya elects to celebrate New Year's with Shiki instead of his family, which makes his sister Azaka very upset, leading to her spending the holiday with her school friends. As the snow begins to fall, Mikiya reflects on what he wishes for most of all: that Shiki's life be filled with happiness.

The second part in a two-part anime film project adapting the "Sixth Singularity - Divine Realm of the Round Table: Camelot" story from the game.

Before the release of the final 7th movie, a remix work "Kara no Kyoukai Remix-Gate of seventh heaven-" comes out in theaters on March 14, 2009. This remix collection extracts the key themes and scenes from first six movies. The hour long movie is organized in chronological order, beginning from the 2nd movie, followed by the 4th, 3rd, 1st, 5th and 6th. It's a mixture of mostly existing scenes, and some new scenes.