Shirou's influence encourages the shy Sakura to slowly come out of her shell. After a year, Sakura acts like her present day self.
Heaven's Feel II. Lost Butterfly
When Rin and Archer burst in to help Shirou and Sakura, Rin remarks that she and Shirou are in an alliance. However, it was in using Sakura as bait that changes Shinji's designation from pest to enemy. One of several hints scattered throughout that for all Rin tries to be a cold-hearted mage, she truly does love her sister.
Shirou running in to protect Illya right as she's about to be blasted away by Excalibur Morgan, wrapping himself around her to shield her with his own body. He had to have known it'd just result in both of them getting killed, but he couldn't just stand by and watch her die. Thankfully they both get saved by Archer at the last second.
Archer's final moments, where, having just barely saved everyone from the Shadow, very tenderly caresses an unconscious Rin's forehead and wishes her goodbye, both sounding and looking more like the loving Shirou than the aloof Archer. Then he cuts off his own arm to save Shirou's life and give them a fighting chance.
Shirou honestly confessing his love to Sakura and making love to her for the first time.
Sakura calling Rin "big sister" for the first time. Rin's reaction was just adorable.
Shinji meeting Sakura for the first time as children in the Lost Butterfly drama cd. He acts all arrogant and tells her not to annoy him too much. Then as soon as she leaves, it's revealed he's actually happy about getting a little sister. Mixed with Tear Jerker, considering how strained their relationship became in the end.
Heaven's Feel III. Spring Song
Shirou reassuring Illya that everything will be all right before using the arm.
From that same moment, the gentle stare Archer gives to Shirou in his mind, as he sees off his younger self after spurring him to fight on with the iconic line "Can you keep up with me?". Archer NEVER sported such a tender look at his younger self, but he finally does now that he can approve of what Shirou wants to do with himself.
Archer's genuine smile during the "can you keep up with me?" sequence when Shirou first unleashes Archer's arm to fight Berserker. The whole reason Archer allowed himself to be summoned for the Grail War was to stop his past self from following his own self-destructive ideal, and at this moment he is able to witness Shirou throwing that ideal away to protect the person he loves. Even though it resulted in his death, Archer ultimately obtained what he wanted after so many untold years.
When Berserker gets offed by Nine Lives Blade Works, the black cloud of miasma fades away, revealing his very rough features, and as he gazes upon a sad Illya, he acknowledges Shirou with these words: "Protect her for me..." just before disappearing.
Rin is about to go for the kill against Sakura after pretending to be unable to care about other people's pain, and she remembers when they played cards as kids... She had such a good hand it was not even funny, and that memory is what spurs her to not deal the final blow because she couldn't bring herself to bring down someone who tried their hardest and crush all their hopes.
Shirou as he both chides Sakura, proceeding to do a Declaration of Protection, and tells her to live on to take her responsibilities for those she has killed.
In a weird way, Shirou, as he finally develops a kinship with Kotomine over their common nature as twisted human beings seeing themselves as sinners and trying to cope with their existential dilemmas.
The fight is nearly over, Shirou only has to project once more to bring down the manifested Avenger, but he is understandably terrified of going through with the gesture as it will certainly be fatal to him. Illya appears in the Dress of Heaven and gently reassures Shirou that she will make sure he lives through this. She is the older sister, after all, so she has to protect her little brother.
The fact that Illya's last words to Shirou are acknowledging him as her younger brother. It shows how far their relationship has come from their first battle.
Illya running into the Holy Grail and embracing Irisviel who is there with arms outstretched to welcome her, contrasting Fate/Zero's Holy Grail.
Shirou reaching out into the white void as the light of the Holy Grail being sealed away consumes him... and Archer grabs his arm and pulls him out, symbolizing that Shirou has successfully fought his fate to become Archer and that Archer is So Proud of You.
Even better: Archer is finally free. While floating in the void, Rin's pendant aka Archer's summoning conduit shatters. When Archer grabs Shirou's hand in the void, they both disappear into a light blue shape that resembles how the Counter Force appears to its contractors before it too disappears in a burst of light. Archer was able to free himself from his contract and no longer has to act as a Counter Guardian.
Another potential implication from the animation is that Archer's being and Shirou's have completely melded together, to reform a complete soul that will now be able to enjoy a happy life.
Sakura and Rin making up for their lost time as sisters, as they travel to find a new body for Shirou.
Sakura has a small shadow familiar happily dancing here and there, acting without any regard for the mood, and quite a bit out of place compared to the more terrifying shadow giants. It likely is the manifestation of her innocence and humanity and is generally helpful and a cheerful presence. We even see him happily propped on Rider's shoulder at the end.
In this scene where we see the small shadow on Rider's shoulder, we also get to see Sakura's face when she turns to Rider (and the camera). You may notice that her irises are blue: not the natural Tohsaka teal color like Rin's, but not the violet color like it used to be either. She even has actual pupils again. Likely a symbol for Sakura's trauma: it would never really leave her completely, but at least some part of her is gradually getting better.
