fate
The story begins with Shirou accidently invoking Saber (since he was in the
verge of a battle against Lancer and almost killed by him) and making her
his Servant. He is introduced to the Holy War by Rin who lets him know about
the rules of the conflict, and he soon realizes he wishes to stop this cruel
game.
In the meanwhile other Masters and Servants appears, willing to take him
down immediately, especially Shinji Matou, one of his friends and classmates,
and master of Rider, who placed an evil seed at school, willing to gather
energy in order to become the strongest (and use her Noble phantasm to dispose of Pegasus). Shinji is eventually defeated by Shirou (although we learn he's killed by Berserker) as well as Saber eliminates Rider although she runs out powers since she used her Noble Phantasm Excelibur even if she knew she couldn't afford it, being an incomplete summoning.
Shirou is lately kidnapped by Ilya and brought to her castle, implying Rin, Archer and Saber to go there in order to rescue him. Archer sacrifies himself in order to let his friends escape and in the attempt to defeat Berserker (he kills him about 6 times, but Berserker's Noble Phantasm let
him survive), but he died before having the chance to kill his enemy more times.
Ilya and Berserker chase Shirou, Saber and Rin as they're trying to escape (and in the meanwhile Shirou replenish Saber's mana having a sexual intercourse with her, as Rin suggests them) and they are eventually caught. Rin fights against Berserker, togheter with Saber, but the decisive resolution comes when Shirou uses his tracing powers to make Caliburn and fights against the enemy with Saber's help and experience. Ilya joins Shirou once Berserker is defeated.
The following enemy to defeat is Caster who made a pact with Asassin and
uses him as her own servant as well. They attack Shirou's mansion in order to get rid of him and his friends. Anyway Gilgamesh's sudden appereance destroies their plans as they're all defeated by him.
The new servant is known by Saber who states that he was involved, as her, in the previous war, also revealing that she was Emiya Kiritsugu's servant.
She also adds that the conflict wasn't won by anyone because she was ordered to destroy the Holy Grail.
Shirou needs advices on what to do next and he wants to ask for Kotomine Kirei's help. He goes to his Church to find replies, and he only find out that he has been joking since the beginning, since he actually is the the master of Gilgamesh and Lancer and he tries to take them down in any way. Kotomine is ready to do anything to obtain the Grail, even kidnapping Ilya, who's the Grail Vessel. He's eventually defeated by Shirou who finally destroies, with the help of Saber (who eliminates Gilgamesh), the evil content of the Grail itself.
The ending could be classified as good, since Saber realizes she doesn't really want to change her "story" and remake the King Selection, and she comes back to her time, accepting her imminent death (and continuing her dream).
unlimited blade works
This time the initial enemy is Caster and her master Kuzuki Souichirou. Caster has gathered a large quantity of mana by sucking it from the towns people and through this she was already able to defeat Rider. At first Shirou and Rin are still enemies but they agrees on the need to defeat Caster and they cooperate in order to defeat their common menace.
Caste, who's able to break the contract between Masters and Servants through her noble Phantasm, attacks the Emiya residence and she's able to erase the agreement between Saber and Shirou, mainly because she's interested in getting Saber and use her as her own servant. Rin is there too, but with everybody surprise Archer betrayes her and decides to join their enemies's side as well.
Rin and Shirou realize they're too weak to stand against Caster and her group. They decide to ask for Ilya's help, but as they arrive to her castle they find out that she has been defeated by Gilgamesh, who suddenly attacked her and Berserker.
Lancer decides to help the heroes too, joining them as they try to defeat Caster and her master. Anyway, before the servant is able to defeat the group, Archer turns against her and eliminates her. He then attacks Shirou with the aim to kill him.
At this point Rin and Saber make a new contract in order to rescue him from a certain death. They're successful and we can learn something more about Archer and we discover he's none else than Emiya Shirou, or well his future (disillusioned) self. He desperatly tries to exterminate his past as well as himself and that's why he's always trying to take Shirou down. His reasons are hard to understand, although he states he hates heroes (and Shirou wants instead to become one).
They fight each other once again: Shirou tries to convince Archer to still believe as the servant only want to end his miserable existence. Only Shirou can defeat Archer, because he's the only one who can make him understand his mistakes and embrace once again his ideals.
Archer seems to accept this and drops the battle withouth saying a word.
Only Gilgamesh is left. Shirou, who can count on his new founded courage and determination, confronts him by releasing his own Unlimited Blad Works, but the deciding action is taken by Archer, who sacrifices himself to protect his old friends and his previous self.
This scenario has two available endings. The normal one which features Saber staying in the present time, living happily with Rin, and the good one which sees Rin leaving for London and Shirou following her apprentice.
heavens feel
The war spreads even more in this scenario. We see most of the servants defeated since the beginning by the Shadow brought togheter with True Assassin, a new servant summoned by Sakura's Grandfather, Matou Zouken, summoned when he finds out that Rider was defeated by Saber, and also Caster follows the same fate. True Assassin appears when also Lancer succumbs after Assassin's attack and he's created from those two servants, or well from what remains of them. Even Shirou loses Saber, as she's devoured as well by that mysterious Shadow which goes togheter with their enemy.
Shirou still wants to fight the war, although he hasn't a servant anymore to fight with, mainly because he doesn't want anybody else to die and stopping the killing is his main aim.
Shirou and Rin join forces again, but their alliance breaks almost immediately, since Rin wants to eliminate Sakura (who reveals herself as the Shadow) and instead Shirou is willing to
protect her (as he realizes she's the person he most loves) He has to make a choice: saving people and sacrificing her love, or doing the opposite: he obviously choses for Sakura's sake.
Sakura has actually a sort of worm that oblidges her to fight in the war in order to survive and not being killed by the magical instructions given to her nervous system.
Sakura has to join the war and fight, sucking life from others to supply her mana needs.
Since Shirou is interested in saving Sakura, Rider, who's still alive since her master hasn't died, wants to make a temporary alliance with him, supporting him from now on.
Shirou tries to get the help of Ilya, but when he meets her they're attacked by the Shadow and they loses the battle, causing the disappearence of their servants and a big loss for Shirou too (he loses his left arm, though Archer supplies him with his, as he disappears because of his defeat).
The group plans to solve the situation by tracing the Jeweled Sword Zelretch, thanks to Shirou's amplied abilities. Anyway Ilya warsn Shirou to be careful in using Archer's arm, since it continues to wound him, due to the fact that it created Unlimited Sword Works inside his body and not outside.
The group is ready to confront Zouken, but they find out it's useless, since he has no controlls on the shadow and he cannot stop it. He reveales many truths about the situation: the worm in Sakura's body is the Vessel of the Grail and that the Shadow is none else than the evil content of the Grail itself, tainted since the 3rd War. He also tells the group that they need to kill Sakura in order to stop the Shadow itself. Shirou has a hard time in listening to this confession and in definetly deciding for Sakura's safety, betraying the sence of Justice and his ideals (and taking a different path from the one he choses previously).
In the meanwhile Sakura is realizing what's happenning, and that's she going out of control (especially when she kills Shinji). She takes consciousness of her situation and she turns to her dark side, willing to go on with the war. To complete the Grail Ilya is needed and that's why she kidnapps her.
Shirou makes a temporary alliance with Kotomine Kirei to rescue her and rejoins with Rin too.
Shirou is able to defeat Black Berserker, by releasing the power of his arm, although this starts a sort of self-destruction process. Kotomine Kirei confronts Matou Zouken. He's able to purify his soul and free him from his "vampire" like status but in his attempts he's critically wounded by Sakura. Ilya reveals to the group that the tainted substance of the Grail is Angra Manyu, a servant summoned by her family during the 3rd War and she states they need to kill Sakura before the Grail is completed, although Shirou doesn't agree with the idea.
In the meanwhile Sakura has devoured also True Assassin and she got rid of the worm implanted in her body.
During the decisive battle, the heroes manage to defeat all the black servants and thanks to Rin indecision (sakura is her sister and she doesn't want to kill her after all) they let Sakura realize her mistakes and eventually save her. Shirou desperately tries to destroy the Grand Holy Grail with his last energies (after the fight with Kotomine Kirei, who turned once again as an enemy) knowing he wouldn't survive...
There are two possible endings at this point. The first one with Shirou sacrificing himself as he detroyes the Grail. The second one with Ilya sacrificing herself for the sake of her friends and an happy ending for Shirou and Sakura.