After Saber’s disappearance, Shirou Emiya is effectively eliminated from the Holy Grail War, but intends to continue fighting regardless. After returning from a meeting with Rin Tohsaka, Shirou finds Sakura Matou has been kidnapped by her brother Shinji and the two confront him. Sakura pleads for everyone to stop and Rider heeds her call, revealing Sakura as her true Master. Faced with the reality that he will never be a Magus, Shinji douses Sakura with a potion that makes her lose control of her mana and flees. Archer and Rin attack Sakura, but Rider defends her and starts turning them to stone with her gaze – revealing her identity as Medusa. However, when Shirou is hurt and loses consciousness, Sakura’s grief causes her to injure herself, forcing Rider to stop.
Shirou reawakens in Fuyuki Church, where priest Kirei Kotomine operates on Sakura. He explains Sakura’s body is infested by Zōken Matou’s Crest Worms, which feed on her mana by arousing her. As Rin contemplates killing Sakura for the danger she poses, Kotomine reveals to Shirou that the two girls are blood sisters with Sakura having been given to the Matou family for adoption. Despite Sakura’s attempts to push him away for his own safety, Shirou promises he will protect her even at the cost of his ideals. Sakura then moves back to the Emiya household with Rider, who slowly starts to trust Shirou. However, Sakura becomes increasingly aroused due to the Crest Worms and her behavior becomes erratic.
Shirou and Rin seek out Illyasviel von Einzbern to form an alliance, but find her in battle with Zōken and the shadow, which unleashes the corrupted Saber Alter to subdue Berserker so it can devour him. While Archer is able to drive Zōken’s Assassin off, the shadow mortally wounds him and severs Shirou’s left arm before retreating. Before dying, Archer cuts off his own left arm and transplants it onto Shirou to save his life. Having lost their Servants, Rin and Illya move into the Emiya household to plan their next step while helping Shirou get used to his new arm, now sealed with a holy cloth as his body cannot handle Archer’s power within. However, as Rin grows closer to Shirou, Sakura becomes jealous and asks him if he loves her romantically, to which Shirou affirms he does – resulting in the two having sex.
One night, Sakura sleepwalks throughout the city and kills several people. The Servant Gilgamesh attacks her, but the shadow devours him. Sakura then returns to the Emiya household and Shirou realizes the shadow comes from her. Bedridden from injuries inflicted by Gilgamesh, Sakura is told by Illya that she has become the vessel for the Holy Grail and thus does not have long to live. Later, Illya – who is secretly Kiritsugu Emiya’s biological daughter and thus Shirou’s adoptive sister – overhears Taiga talk about Kiritsugu and lets go of her grudge against him after learning he tried to return to her before his death. Meanwhile, Shirou is approached by Zōken, who reveals the shadow is a piece of the Holy Grail from ten years ago that he put inside Sakura and is not his ally – in fact, he can barely keep it contained. Zōken tells Shirou the only way to stop the shadow is for him to kill Sakura, as he is the only one she trusts enough to let close, but he cannot bring himself to do it.
Seeing herself as a burden to Shirou, Sakura orders Rider to protect him and returns to the Matō estate, with Shirou giving chase. However, Shinji attempts to rape Sakura once she arrives, blaming her for his inability to become a magus. Threatened with Shirou discovering Shinji has raped her for years, Sakura panics and kills her adoptive brother. As Sakura realizes what she has done, the shadow fuses to her body and corrupts her.