How Sakura first saw Shirou is this when you take into account her Dark and Troubled Past. As Sakura herself said, back then she wished for nothing but for Shirou to fail in doing the high jump, and yet as she watches on Shirou just keeps on trying, no matter how many times he failed. In the end, Shirou failed to do the high jump, but from how Sakura tears up and how fondly she recalls the memory, its clear that the scene became an encouragement for her to keep on going with life even if only failure awaits her at the end of the line. The fact that seeing such a simple scene manages to evoke such a reaction from Sakura (in contrast with Rin's reaction to seeing the scene) is just heartbreaking.
Rin and Archer's discovery of Sakura's "training" room could definitely qualify for both of them. Rin is forced to learn just what kind of hell her little sister has been living through for the past eleven years. And while we don't know exactly how Shirou became Archer, he's either discovering this and learning just what kind of life Sakura was forced into while she kept up a brave face for him, or he is being forcibly reminded of it.
Since the movie heavily implies that the choice Archer made that resulted in him being so different from the present Shirou was killing Sakura when her powers went out of control, he's getting to see what the girl he cared for actually went through to drive her to that point.
Nasu and Takeuchi talk about Sakura wearing a short-sleeved dress in a cold February night during the scene in the storeroom with Shirou in an interview included in the Blu-ray: Is she cold? Of course she is! But she wants to look cute for Shirou. And for her, this cold is just "cold", but is not hard or painful for her compared to the torture that she is going through everyday...
The shot clip of Issei crying when informed about Kuzuki's death.
Heaven's Feel II. Lost Butterfly
Taiga asking Sakura if she has a hero she admires just as Shirou admires Kiritsugu. As Sakura contemplates an answer (that she doesn't come up with), she fiddles with her hair ribbon... which Rin had given to her.
Archer dying. After a desperate battle with Assassin, he's badly injured and so is Shirou, who has lost one of his arms. With Tohsaka unconscious, Archer (with his hair down, like a certain someone...) softly caresses her face and bids her goodbye before walking a short distance away to cut off his arm for Shirou. When Rider points out that this'll kill him, he responds that it doesn't matter since he's dying anyway, but he's giving them a chance to survive. The camera cuts to black just as he strikes his arm.
Sakura's reaction to Rin revealing that she too saw Shirou attempting to make the high-jump. Especially with the context that Sakura fully believed that one day Shirou would leave her and that their time together was fleeting. That Rin herself might one day be the one to gain Shirou's affections. For Sakura, that was a special memory that gave her the will to feel like a human once again no matter the pain. And hearing that it wasn't just her memory, that the sister that she idolized and envied also had it meant that it was no longer just hers.
Shirou deciding to kill Sakura, taking the knife out from the kitchen and raising it above the sleeping Sakura. And then memories of his time with her flashed through Shirou's mind, along with memories of Kiritsugu; his hand trembled, and then we got a shot of Shirou crying his eyes out, clearly conflicted and in pain of wanting to fulfill Kiritsugu's dream and become a hero of justice but not being able to bring himself to kill the girl he loves. And then he lowers the knife, walks away, and confirms to himself that he'll betray his ideals, the very same he had stubbornly kept in the past two routes, for Sakura.
Making this scene extra heartbreaking is this is the first time we see Shirou truly cries. We've seen how stubborn and hard-headed Shirou could be in trying to pursue his ideals, but this is the first time he actually breaks from the sheer unfairness of the situation he faced.
Adding to this is the fact that Sakura was awake through the entire ordeal, merely faking her sleep. She was ready to accept Shirou's decision, even if he were to kill her, and when he doesn't... tears fall from her eyes as she realized just what she had done to the man she loved. The entire thing is just so unbearably tragic for all parties involved.
Heaven's Feel III. Spring Song
The opening of the movie has Shirou finding Shinji's dead body in the aftermath of Sakura's fall into darkness. While Shinji was a nigh irredeemable person and a complete monster given his treatment of Sakura, he was still Shirou's childhood friend. At the very least Shirou was there to brush his eyelids shut given how Zouken left him to rot.
In the third movie, Illya tearfully asks Shirou why he has to risk his life to fight, when he has done nothing wrong. Shirou retorts softly that he did do wrong (allowing Sakura as the shadow to live, knowing that people were dying en masse but still choosing Sakura regardless) but ultimately wishing to go through with this in order to protect Illya, stating that it's the older sibling's job to protect the younger one. It is clear on Illya's face that she wants to correct him and tell Shirou that she is the older sibling, but she can't bring herself to do so. Shirou then proceeds to undo the seal on Archer's arm, which will condemn him to a slow and excruciating death.
As he goes to fight Berserker, in a split second he analyzes his weapon and extracts its history...viewing the Twelve Trials Heracles went through...culminating in a scene where a still living Heracles holds his dead children in his arms, unable to hold back his tears and screams of anguish. This moment alone reveals to us that Heracles wanted nothing more than to be able to protect a child that would call him "Father." It also adds another layer to the hero, showing that there is more to him than just a hulking brute.
Heracles stops his killing blow on Shirou, despite this meaning that it would have resulted in a draw. The reason? He sees a terrified Illya, holding back her tears as she sees her father figure and adoptive brother fight each other to the death. As he's about to fade away, Heracles regains his sanity for a few seconds, leaving these last words to Shirou: "Protect her for me..."
In the flashback of the conception of the Greater Grail, Justeaze sacrifices herself, mercilessly crushed by the crucible pillar that would turn her into the circuits for the magecraft circle. Zouken looks on, keeping a stoic front, though his expression shows he clearly does NOT take it well, reiterating his oath to reach the Root and liberation from the shackles of mortal condition, with visible anguish.
After offing Zouken, Sakura has a Laughing Mad fit, realizing she is finally free... before she has a And Then What? moment. Even Saber Alter is at a loss for words on how to comfort her, despite her now permanent stoic nature.
When Shirou declares his intention to kill Saber Alter, she just...smiles, because her former Master has essentially sworn to end her torment.
Saber Alter's death at Shirou's hands. Rider lands her Noble Phantasm Bellerophon on Saber head on after the dark Servant's own Excalibur Morgan's attack was stopped by Shirou's incomplete Rho Aias. Broken and defeated, Saber struggles to rise but can't, giving Shirou the opportunity to land the finishing blow. Saber's reaction is a dazed uttering of her former Master's name and it is jarring how confused and innocent she sounds, implying that the original Saber is still in there. Shirou's face is one of complete anguish, and although he would like to stop, he proceeds with the finishing blow, stabbing her right in the heart.
Compounded by the eerie calmness Shirou emanates as he tells Rider to catch up with him once she has healed. It is truly a sight to behold the Death Glare Shirou sports after the act, likely utterly broken inside at what he was forced to do, but still determined to see things through.
Sakura's reaction as she stabbed Rin, her sister, who never stopped caring about her. Rin herself realizing that she didn't have it in her to stab and kill Sakura. Both sisters are in tears for the situation they found themselves in.
Sakura crying and begging Shirou to leave and just let her die.
Shirou crying while saying that he wants to live. For everything he has done up to that point, it's easy to forget that he's still just a scared teenager.
To make matters worse, using Archer's arm actually destroys his body and brain the more he uses it, as shown when he could barely remember Rider's name. By the time Illya stops him from sacrificing himself, Shirou can only remember his sister's name out of pure instinct.
Illya sacrificing herself to shut down the Grail and thus close the gate to the Root, and reuniting with her mother in death.
Shirou's reaction to this happening is heart-wrenching. Kudos to the seiyuu for voicing Shirou's lamentation as he struggles to remember Illya's name due to overusing Archer's arm, his own self-hatred at wanting to live despite knowing he had to sacrifice himself to destroy the grail, and reduced to screaming and crying for the girl to come back, shouting Illya's name over and over again.
