A fleeing Shirō is eventually cornered by Rin, who offers to spare his life if he gives her his Command Seals. However, he refuses, prompting Rin to try and kill him. Both are then distracted by a scream downstairs and he and Rin find an unconscious girl. As Rin attempts to heal her, a dagger flies through an open door, aimed for Rin, but Shirō blocks it with his arm, wounding himself in the process. He runs outside to find the female Servant, which is of the Rider class, and repels an attack by her. Shirō considers summoning Saber via Command Seal, but decides it is too risky to get her involved and resolves to confront Rider himself. Rider resumes her assault, and Shirō is nearly killed by her until Rin rescues him. At Rin's home, Shirō and Rin decide to form a temporary truce to find Rider's Master.

Saber yelled at Shirou for not summoning her when he was in danger. Saber starts to go to school with Shirou. When Rin appears and says she will walk with Shirou to school, Saber allowing this after Rin talked to her. She explained that this way enemies may think it's a trap to not see Saber with him so they are less likely to attack.Rin explains that there should be spell marks around the school and if they destroy those it will delay the activation of the force field but not destroy it, and most likely force the master out of hiding. After school Shirou and Rin work to find spell marks and destroy them. They end up destroying a good amount of them and call it a night.On the way home, before Shirou gets anywhere but after Rin leaves he feels something really strong. He goes to investigate it and feels its coming from the archery club.

Shinji says things like how he has no intention of fighting and he was just dragged into this war. He asks to make an alliance with Shirou to go after Rin but Shirou refuses. Shinji says because he doesn't know magic other Masters can't detect him so that means Shinji isn't the other Master Rin was detecting, meaning there is a fourth one at the school. Before Shirou leaves Shinji tells Shirou about how one of the Masters has set up base at a temple.Shirou gets home and is yelled at by Saber and Rin, Rin having come over after Shirou didn't come home. Shirou tells them about Shinji and the Master at the temple.Shirou and Rin both agree, against Sabers judgment, that they should not attack the temple yet as they don't know what Servant and it may be a trap.Saber brings up again with Shirou the temple but Shirou insists that they won't be going.

Saber is eager to go to the temple but Shirō has insisted that they won't be going because it seems too dangerous. Nonetheless, as soon as Shirō falls asleep, Saber heads off by herself to the temple, not only to be confronted by the servant identified as Assassin. Unlike any other servant, Assassin actually reveals his true identity to Saber, as Sasaki Kojirou. Although the talking ends here and the fighting begins but while this is going on Rider sneaks past them and enters the temple to fight some woman. Who is this mysterious woman and was Shinji planning this all along?

After a mornings training session with Saber, Shirou is then straightaway dragged off by Rin for some more training of her own. While this is going on Shirou receives a phone call from Shinji, asking Shirou to meet him at the school. Because it seemed urgent Shirou heads of to school and is greatly shocked by what he sees. Shinji shows his true colors and says how he wanted to show Rin how he was superior to Shirou and that he would defeat him here. What will happen to Shirou and does he have the will to fight off a Master and his Servant, alone?

Shirou is very worried about the well being of the students, staff, and of the school after yesterday's events, he's especially worried about Taiga who seems to be recovering well. Shirou is now determined to put an end to this and plans to go after Shinji before he can make another force field and with Sabers support they head out. However before that, Shirou has some important information to disclose to Rin about Shinji's Servant, Rider about the Noble Phantasm she used.

Shirou falls asleep and sees a dream of a flashback of Saber's past. We see Saber in plain olden time cloths walking up to a sword in a stone.Saber wakes up and notices Shirou is gone. She talks to Rin and despite Archer's objection they go looking for him, suspecting he has been kidnapped by an enemy.Shirou wakes up in Ilya's house as her captive. Ilya says how she wants Shirou to become hers.