The movie begins with Shirou dreaming about the previous movie's temple and losing saber there. He chases after her, she's replaced by the Shadow, he's killed by it, and then he wakes up. Shirou then talks to Sakura over food, Sakura laments over how suddenly 'Saber-san' left but is glad that Shirou won't have to go out at night again. Shirou says no, he still has unfinished business and then the movie title drops. It's a lot faster than the first movie as far as I remember.
After that he's shown planning stuff while looking over a town map at a park when Illya hits him in the face with a snowball to get his attention. They sit down and talk after Shirou panics over them being enemies. Illya jumps onto his lap (actually she just leaps onto him, full body and all) (this was super cute btw) and says you know, she could kill him anytime anyway so why not. They talk a bit and then Shirou asks if Illya recognizes the name Emiya Kiritsugu. She becomes downfallen immediately, says she doesn't and leaves. Shirou tries to catch up to her but finds she's disappeared before he knew it, and then runs into Rin so they go to Rin's place to strategize. There, shirou sees a picture of young Rin and notices her ribbons (which is Sakura's now). Then it cuts to Sakura opening the door at home to someone after waking up from a dream about her being left behind. Then it cuts back to Shirou running back home while mentioning something about Sakura and Rin's right behind him. He comes home to find Sakura, gets a call from Shinji (it cuts just before he actually picks up), then he runs out of the house to school.
The confrontation with Shinji and Rider that follows happens 10 minutes into the film. It takes place inside a library instead of the hallway but is pretty much the same as the VN. You can tell Rider was helping out Shirou by going easy on him, and Shinji's pretty well directed here, for example. After Shinji breaks the ear ring bottle, Sakura becomes uncontrollable and weird magic spikes explode around her randomly. Archer tries to approach Sakura, Rider kicks him away, they talk and Rider uses her Mystic Eyes, freezing Archer, Rin and Shirou in place. A spike ball appears next to Rin and it was about to expand/explode. Shirou pushes her away and gets impaled, he blacks out. He wakes up in the church and basically this scene the same as the VN as well. Kirei explains loudly what's going on, reveals Rin and Sakura are sisters, Rin declares that as the one in charge in this city she has to eliminate Sakura, they go inside and see Sakura's run away.
Shirou goes out in the night to find Sakura before Rin does. He runs into Illya. Here Illya gives him the 'watashi wa shirou no mikata' speech and admits she really did know Kiritsugu. She pats him on the head and stuff. Shirou goes to Sakura, embraces her (we get a bit of monologue-ing here and some inappropriately smooth animation for just him walking towards Sakura) he gives her back the house key she dropped earlier, Sakura admits she's not a virgin, etc. etc. it's like the VN. They walk, hand in hand, past Rin and Archer who didn't stop them. Archer says out loud that he better commit to that path and not go off it. At home, Sakura says she needs blood to refill her magic, Shirou bites his finger to get blood out and lets Sakura lick it off and he's obviously flustered by how lewd Sakura looked while doing that. They included the breakfast scene with Rider the next day (cute) where Shirou tries to make her feel welcome. Just a little later we get a Sakura masturbation scene after Shirou and Rider leaves to meet Illya to cooperate. It's not that lewd, she falls to the ground, we see her hand move to her crotch area and her other hand fondles her own chest and it blacks out and comes back to after she goes to the bathroom to wash off the worms. We see her reflection in the mirror saying things Dark Sakura would.
At Einzbern Castle, Shirou stumbles into a scene with Zouken and Illya while hidden. After some shit with Zouken, Salter appears to fight Berserker. This is a pretty long fight scene, comparable to True Assassin vs Lancer but I like it a lot more here. This is the best portrayal of Berserker in combat imo. You can tell he's the one being BTFO'd by Salter despite him doing so much moving and attacking that he feels really powerful while making Salter even stronger. Salter's Excaliblast is super well animated too. When I say the first half of the movie is action heavy I mean this fight. Berserker's my personal MVP this movie (Sorry Shinji you're only second place this time) even though I can't care less for servant action scenes in general. Enough of my thoughts, other details include: They reproduced this CG pretty well
https://vncg.org/fsn/775. Rin shielded Shirou from the blasts caused by Berserker vs. Salter. Then Archer appears and he fights True Assassin and that is juxtaposed with Berserker vs. Salter. Illya's alone on top some kind of platform and just before the blasts hit her, Shirou runs to her to hug/protect her. Then it was Archer who dragged them both out before the blast hit them. Archer tells Shirou to protect Illya properly. They run away and fight off True Assassin until Archer makes TA retreat. Then the Shadow appears right next to Rin and Archer rushes to protect her, getting impaled in the process. Archer uses Rho Aias against the huge-ass magic blast the Shadow was about to fire. The screen flashes, then we see the entire area destroyed pretty badly. Archer's heavily injured, his hair is down and he's recognizably Shirou now. Rin's on the ground next to him, unconscious, not too inpured. He hears Illya shout 'Shirou', he turns around and sees Shirou's unconsicous on the ground, his eyes left open and his arm is vaporized, only a pool of blood left where it used to be. Archer acknowledges that it's time, draws his sword out and prepares to cut his own arm. Rider manifests and questions him. He doesn't stop. Blade sinks into his flesh. Black screen.
Literally the next frame Sakura opens the door and sees Shirou back with Archer's arm on him, covered in the shroud of Martin. He apologizes for looking this bad but he's alive and stuff, and Rin and Illya are with him. Basically they FUCKING CUT OUT KIREI AT THE CHURCH SAVING AND EXPLAINING THE ARM TO SHIROU. Instead this stuff is explained by Rin just a little later in a voice over. I'm not as mad as I sound, I was just really surprised because I thought Shirou getting Archer's arm was going to be where the second film ends off. Imagine my surprise when this is probably like halfways through the film. There's a good scene of Shirou in the bath where he tries to loosen the cloth just a bit and his mind almost breaks because of that.
The second half of the film is much better i think, it's a bit slower. we get Shirou and Rin talking in the shed and Sakura eavesdropping so she hears Rin confessing that she knew shirou ever since the running scene 4 years ago and cries cuz NTR. That same night she goes to Shirou's room out of desperation after hearing Rin confess about that. She went there and instead of lifting her skirt like in the VN, she strips to her underwear but since Shirou's back was turned to her because he was looking through the drawer for something, he doesn't see this. She embraces him from behind and asks why he's protecting her. Shirou says it's because he loves her, then she asks him to turn around to see her. She says that it's because she's already defiled that it's making this whole thing weird. Shirou says not at all, they kiss and fall to the bed and have sex. it's not that lewd, we get handholding, sideboob as she embraces Shirou in the nude after they were done and that's it.
We get Sakura calling Rin nee-san as they cook next morning. we get a bit of a montage afterwards I think where an accoustic/orchestral version of hana no uta (i dont remember which because we got both) plays while Sakura talks to herself. One of the scenes in this montage is Shirou and Illya walking home singing that german tune of hers so i'm really frustrated with that being waved away like that. Another scene in the montage is Illya and Rin making Shirou conjure up a sword, although it's not the Jewel sword.
Somewhere around here we get a scene of Kirei talking to Gilgamesh. It's like at least a minute long but I wasn't listening too well at what they were listening. Then we get a really nice Alice in Wonderland-esque dream sequence with Sakura which then cuts to Gilgamesh confronting her and the candy Sakura was eating in that dream turned out to be a piece of flesh from her victim. Gil skewers her with GoB, cutting her hand off and leaving her a bloodied mess on the ground and then he then jobs like the irrelevant dumb villain he is. Sakura goes home, bloodied, Shirou finds her at the doorstep and hugs her. Here he narrates how he mustn't realize what's going on here. Do not notice how similar Sakura is to the Shadow. Like that.
Later Illya comes into Sakura's room to tell her how she'll die because as a grail, she already got all the mana/heroic spirits she needed despite Rider and True Assassin being alive. Taiga comes to visit Sakura so Illya hides. Illya eavesdrops in on Taiga talking about Kiritsugu having a loved one he tried to reach even at the very end of his life, so even Shirou must have a loved one as well even if he's trying to be a seigi no mikata. This calms Sakura down a bit.
At some point Shirou talks to Rider. Rider says she likes Sakura and questions if Shirou will be by her side. At some other point Shirou is called by True Assassin to talk and Zouken reveals the truth of the shadow. Later at night, Shirou comes in with a knife and tries to kill Sakura. He then has flashbacks to all the events with Sakura so far and decides he couldn't do it, puts his knife down and declares he'll 'betray his ideals' as he walks out of the room. Sakura was actually awake through all this. I guess this is like the climax of the film. She wakes up the morning after, leaves her key on the desk, meets Rider at the gate where she thanks her for not killing Shirou and uses up her last command spell and leaves.
Then it's her at home and Shinji comes in and they talk. For some reason Shinji tries to butter her up by piling on compliments about how sugoi she is and how she's better than Rin. He hands a small vial of something to her that he says isn't harmless, and it shines when Sakura's holding it. For some reason that makes him smirk, he walks over to Sakura and slaps her, saying don't get cheeky, she'll never be better than Tohsaka. Shinji pushes her down and tries to strip her. Sakura was thinking she'd just bear through it ('gaman') but then Shirou flashes in her mind and she pushes Shinji away, that made him lose his temper and he tries to rape her more violently and that's when she came to think that there's no reason for someone like him to live. Ribbons come and kill him really, really abruptly and unceremoniously like in the VN. They reproduced this CG too
https://vncg.org/fsn/789. Seeing her nii-san dead on the bed, she slowly breaks down as she starts seeing those weird golem-like figures that you see Rin destroying with the jewel sword way later on in the VN, dancing around the corpse and herself. She transforms into Dark Sakura. All this is juxtaposed occasionally by Shirou running towards the Matou house, and the last shot is Sakura's lips giving a menacing smile.