After Saber Alter's disappearance, Shirou Emiya, Noriaki Sugiyama, remains determined to press on in the Holy Grail War, even as the reality around him grows bleaker and the rules tighten. Returning from a tense talk with Rin Tohsaka, he learns that Sakura Matou, Noriko Shitaya, has been kidnapped by her brother Shinji Matou, Hiroshi Kamiyaami. The desperate plea from Sakura draws Rider, Yuu Asakawa, into the fray, and Rider reveals a startling truth: Sakura is her Master. The revelation changes the battlefield instantly, and Rider’s protective power begins to tilt the balance as she uses her stare to turn enemies to stone, exposing Sakura’s hidden powers as Medusa in a living test of allegiance and danger. The clash escalates quickly: Shirou is wounded and unconscious, and Sakura’s grief-driven breakdown forces Rider to intervene and halt the chaos.
Shirou regains consciousness at Fuyuki Church, where the enigmatic priest Kirei Kotomine, Jouji Nakata, explains Sakura’s dire condition. He reveals that Sakura’s body is infested with Crest Worms of the Matou family, creatures that feed on her mana by fueling her vulnerabilities. Rin, weighing grim options, contemplates killing Sakura to avert the looming catastrophe, but Kotomine’s unsettling truth shakes the room: the two girls are blood sisters, with Sakura entrusted to the Matou clan for a reason. Sakura resists Shirou’s pleas for safety, yet he vows to protect her even at the cost of his own ideals, a promise that makes Rin pause and doubt but still choose to stand by him. Sakura returns to the Emiya household with Rider, who slowly starts trusting Shirou as they navigate a future that neither of them fully understands. Yet Sakura’s condition worsens as the Worms awaken new, volatile desires within her, pushing her behavior toward the unpredictable.
Meanwhile, Shirou and Rin seek a powerful ally in Illyasviel von Einzbern, Mai Kadowaki, only to find Illya clashing with Zōken Matou and the ominous shadow he unearths, an ominous force that unleashes a corrupted Saber to subdue Berserker, so the shadow can devour him. Archer, Jun'ichi Suwabe, manages to drive away Zōken’s Assassin, but the shadow wounds Shirou so severely that his left arm is severed. In a selfless and almost mythic turn, Archer sacrifices his own arm and transplants it onto Shirou, saving his life but leaving Shirou to cope with the power now sealed in his body by a holy cloth. With their Servants gone, Rin and Illya relocate to the Emiya home to plan their next move, while helping Shirou acclimate to his newly grafted limb and the strange balance of power within him. As Rin grows closer to Shirou, Sakura’s jealousy flares, and she confronts him about love, leading to a charged moment where Shirou confirms his feelings for Sakura, complicating loyalties and stakes.
One night, Sakura’s fragility fractures into a darker edge: she sleepwalks through the city and kills several people. Gilgamesh, Tomokazu Seki, attacks her, but the shadow swallows him. Sakura returns to the Emiya house, bedridden from the encounter, and Illya—revealing her own tangled fate as Kiritsugu Emiya’s biological daughter and Shirou’s adoptive sister—offers a quiet, if strained, acknowledgment of their shared past. Zōken prods Shirou with a stark warning: the shadow haunting Sakura is a fragment of the Holy Grail he placed inside her years ago, barely contained, and the only way to stop it might be to end Sakura herself. Shirou cannot bring himself to such an act, clinging to the fragile hope that protecting Sakura is possible without destroying her.
As the strands tighten, Sakura’s body and mind strain under the Worms’ influence, while Shirou’s oath to shield her draws him deeper into a conflict where devotion tests every limit of courage and sacrifice. The story threads together loyalty, love, and the perilous remnants of the Grail War, painting a battlefield where every choice carries a cost and the line between protector and victim blurs in the shadow of a legend that refuses to die.
