In this route Sakura Matou, Shinji's adoptive sister and Rin's sister by blood, is the heroine. In the beginning, Shirou meets Zouken Matou, Sakura's grandfather. At first Zouken doesn't seem to be interested in the War, but he later summons the True Assassin Servant and is seen around a mysterious shadow. Shirou and Saber encounters Shinji and Rider, when Rider is defeated, Zouken appears to scold Shinji of his failure.
When Shirou and Saber arrives at the Ryuudou Temple, they find Caster wounded and her Master dead. After Saber deals the finishing blow and leaves with Shirou, a mysterious shadow appears to consume Caster. Soon after when Lancer shows up at the temple, he is ambushed by True Assassin and the mysterious Shadow, the latter of which consumes Lancer as well.
When Shirou and Saber decides to investigate Ryuudou Temple further, they encounter Zouken, True Assassin, and the shadow, and Saber is consumed by the shadow. Without a Servant, Shirou teams up with Rin and Rider. Turns out Rider's true Master is Sakura, and that Sakura is actually Rin's sister! Shirou finds out that a worm has been implanted in Sakura's body, and it will consume her unless she participates in the War. In order to replenish her mana, she is forced to take the life force of others. While Rin decides to and Archer decides to kill Sakura before she can cause any harm, Shirou decides to protect Sakura instead of following his ideal of fighting for justice. Sakura and Rider now live with Shirou, with Sakura regularly having sex with Shirou to satisfy her hunger.
Shirou meets Rin on his way to see Ilya, they are distracted by Berserker's fight against Assassin, the shadow, and Saber Alter. While Berserker loses the fight and Archer is wounded protecting Rin, Shirou is able to protect Ilya at the cost of his arm. The group is saved by Rider, and Archer decides to give his arm to Shirou before dying. Both without Servants, Rin and Ilya decides to stay at Shirou's house and work with Shirou to trace the Gem Sword of Zelretch.
In the meantime the shadow continues to kill people at night, and even consumes Gilgamesh. It is later revealed that the shadow is actually Sakura: Zouken implanted the Vessel of the Holy Grail from the previous War into Sakura's body as a worm, and the shadow is the content of the Grail. Presented with a choice, Shirou once again betrays his ideals and choose to protect Sakura. Sakura goes to see Zouken to try to end it all by herself, but instead is forced to kill Shinji, and gives in to her inner darkness. Sakura attacks Shirou's group and takes away Ilya to complete the Grail.
Shirou goes to save Ilya with Kotomine's help. During their escape, they encounter Dark Berserker and Aasassin. Kotomine is able to win his fight, but Dark Sakura critically wounds him by stopping his artificial black heart. Shirou defeats Dark Berserker by activating Archer's arm, which starts to slowly kill him. Ilya explains that the content of the Holy Grail has been tainted since the 3rd War. The group decides to kill Sakura before the Holy Grail completes, but Shirou still thinks he can save Sakura, hearing Shirou's resolve, Rider agrees to help as well. In the meantime Sakura consumes Assassin and kills Zouken.
The final battle takes place in a cave under the Ryuudou Temple, which the original Holy Grail ritual took place. Shirou defeats Dark Saber with Rider's help, and Rin uses the Gem Sword of Zelretch to fight Sakura. Although Rin is able to fight equally with Sakura, she hesitates to kill her, Sakura goes berserk after realizing her sister's true feelings, but Shirou is able to save her by tracing Caster's Rule Breaker. Kotomine suddenly appears to stop Shirou from destroying the Great Holy Grail, but is defeated by Shirou, who then destroyes the Great Holy Grail.
Heaven's Feel has two endings. In the Normal ending Shirou sacrifices himself to destroy the Grand Holy Grail. Sakura waits for his return at his house as years passes by. In the True ending Ilya appears before Shirou could destroy the Grail, and sacrifices herself to save Shirou. Shirou receives a new body from a certain puppet master, Sakura is able to keep Rider around due to her large amount of leftover mana, Rin leaves to study at the Mage's Association.