Shinji is the temporary master of Rider. He is initially depicted as an evil and deceptive character, but as the story moves along his character begins to show cowardly and even pathetic qualities. He tries to partner with Shirou, but he declines the offer. Shinji later finds out that Shirou has already partnered with Tohsaka and gets angered, trying in vain to turn Shirou and Rin against one another.

He later tricks Shirou into coming to school, to trap him there as he forces Rider to activate her Bloodfort Andromeda. Shirou is able to hold on and tries to reason with Shinji, but he does not listen and orders Rider to kill him. Rider's blade is unable to deal Shirou a killing blow, so she kicks him out of the window. Shirou calls out Saber and the two servants fight. While Shirou defeats Shinji, forcing him to call off Bloodfort. Shirou and Saber travel through town trying to find Shinji and Rider but are unsuccessful at first. After finding them, Rider and Saber start fighting and in the end Saber is forced to unleash her Noble Phantasm, Excalibur, to defeat Rider. After losing Rider and his Book of False Attendent is burned, Shinji escapes the building, only to be murdered by Illya and Berserker.

In the Unlimited Blade Works route, he loses Rider when she is killed by Souichirou Kuzuki. Shinji's failure and loss of Rider results in him approaching Kirei Kotomine, who lends him Gilgamesh as a Servant. Some details of his past are revealed, like the fact he hates his father, Byakuya for hiding the truth about the real heir of the Matou family and that he hates his own mother (whose corpse is revealed to be at the worms storage) for giving birth to him without Magic Circuits. Gilgamesh quickly notices that Shinji has no idea about the Grail and realizes that he thinks it is just a game. He takes advantage of it and manipulates Shinji into killing Illya.

After Lancer kills Kirei, Shinji tries to rape Rin (in the visual novel, he also tries to make her partner with him, despite Rin's warnings that he is just being used by Gilgamesh) only to be pricked in the arm by Lancer's Gáe Bolg. He escapes and has a mental breakdown in which he imagines himself ripping off the arms of everyone. Gilgamesh appears and ignoring Shinji's protests, implants Illya's heart inside of him in order to use him as a new vessel for the Holy Grail. It results in him being forced to endure a mass of flesh growing from his body. He is rescued by Rin and is eventually hospitalized. According to Shirou, Shinji returns to his old self, thus getting along with Sakura again.

In Heaven's Feel his past and his torn relationship with Sakura is expanded. After losing Rider, Zouken comments that Shinji is much more worthless and pathetic than Byakuya. This infuriates him and in an attempt to show Zouken that he can be the heir instead of Sakura, he becomes more manipulative, frustrated and violent towards Sakura.

He later tries to take Sakura back home by force only to be stopped by Shirou. The next day, the ill Sakura wants to walk to school with Shirou, but he declines. Shinji takes adventage of this and kidnaps Sakura with the help of Rider, because he has another new Book of False Attendent. He orders Shirou to go to school without Saber if he wants Sakura back. When Shirou arrives to school, he is forced to reinforce himself in order to fight Rider alone. Rider is fairly weakened and starts disobeying Shinji's orders. After Shinji orders Rider to kill Shirou, the hostage Sakura screams and Shinji's Book of False Attendent is burned again. At that moment, Rider becomes more powerful and it is revealed that Sakura is the principal Master of Rider, who was summoned several days prior to the start of the 5th Holy Grail War. However, under pressure from Shinji and the desire not to fight either Shirou or Rin, Sakura yielded her Master's right to him, although Sakura retains her original Command Mantra.

Shinji remembers how his father and sister hid the truth about the heir of the Matou family from him for seven years, which resulted in his father becoming harsh and causing Shinji to hate Sakura. Soon after, Shinji has an ultimate mental breakdown and blames Shirou and Sakura for his disgraces, deciding that he will break Sakura on his own. Sakura arrives in the Matou house in order to find Zouken and to force him into ending her life. However, Shinji appears and tries to rape Sakura again, blackmailing her into staying with him by telling Shirou about her history of being raped by him for the last three years. This ultimately causes Sakura to kill Shinji, and after realizing she is "the shadow", Sakura becomes Dark Sakura. It is eventually revealed that Shinji's actions in the whole route were orchestrated by Zouken in order to further his schemes for Sakura, and that he was being manipulated the whole time.