He lost both of his biological parents to an accident and whilst trapped beneath the scrap and debris, he was saved by Kiritsugu Emiya who later became his adoptive father and mentor.
He followed Kiritsugu to Fuyuki City, to investigate the Sakatsuki family. When they arrived, the city was engulfed by a black shadow. Shirou noticed a pillar of light in the Sakatsuki estate and saved the Child of God from a collapsing roof. Through some unknown means, she was born as the perfect vessel of the Holy Grail.
Learning proper magecraft from Kiritsugu unlike his counterparts, Shirou fought to remove Miyu from the grasp of the Julian Ainsworth and allow her to escape to the other world. He was eventually captured and used as a means of keeping Miyu in check after she returned.
Much like his counterpart, Shirou dresses in a white and blue sleeved shirt and slim blue jeans, albeit both of which are in ragged condition due to his imprisonment. The most notable difference lies in a small streak of white within his otherwise auburn hair as well as several tanned streaks of skin throughout his body, the changes of which most likely came about due to the extensive use of projection magecraft within his own timeline.
In his past, when he was still going to school, he wore the same uniform as his counterpart, along with a scarf. During the 5th Ainsworth Holy Grail War, he is seen with a jacket and most of the time with a coat, who is somewhat similar to the one that Shirou Emiya wears in the Ufotable anime adaptation of Unlimited Blade Works. When he installs the Archer Class Card, he obtains Archer's signature attire but with minor changes like wearing a red headband and being sleeveless on his right arm.
Shirou deeply cares for Miyu and her safety, willingly fighting the Ainsworths entirely for her sake. Although her sacrifice is intended to save the world, he rejects Julian's notion of needing to sacrifice one to save all and decides to accept the "evil" that comes with fighting against him. He greatly belittles himself in his inability to truly save her, calling himself the "worst of the worst."
Shirou was also extremely close to Sakura. He cared deeply for her, but it was unknown if he possessed any romantic feelings for her. Her death gave him the resolve to gain all of the class cards and save Miyu. He is deeply shocked when he discovers that Sakura has been turned into a doll.
Shirou also seems to be a bit more sarcastic and laid back initially than when compared to his alternate selves, often teasing Julian when they were in highschool together. However, this part of him disappeared as the war progressed, mixed with guilt, regret, desperation and biting despair at the lost of his loved ones and at that time also Miyu. Overall, his personality seems closer to EMIYA than to other Shirou Emiya's. Yet, he incorporates EMIYA's dark and ruthless sides more than his lighter teasing sides.
Fate/kaleid liner PRISMA☆ILLYA 3rei!!
Fifth Holy Grail War
Before the Holy Grail War Shirou had a similar life to his Fate/stay night counterpart. He often helped the school council president of his school and is good friends with him. The difference here is that he never quit the Archery Club and that he and Sakura were the only members and he never met Shinji. After Kiritsugu's death, he confined Miyu in the Emiya residence as he had told him and since he didn't know how to treat Miyu after that because of being in conflict with himself. For her education, he gave her books to read while he wasn't home or was training in Magecraft.
Shirou has later on a conversation with Miyu when she was looking for constellation signs and mentions to her that Kiritsugu loved to do that from the spot they were on wondering if he did that because he was making wishes to the stars. Miyu then makes a wish to become true brother and sister with Shirou, which is indirectly granted by herself with her eyes changing colors from red to amber. From there Shirou decided to start over and take her outside seeing that her wish made her develop from being the Child of God into being human.
Going in front of a elementary school and thinking that it could make Miyu learn more about academics or common sense and make friends of her age but then remembers that it will be closing down before the end of the year. He finishes by noticing in the school a little girl but is interrupted by Sakura. During this day he talks with Julian and mentions that he has a little sister and the girl making him overreact by spilling his tea on himself. During their dialog, Julian says to Shirou that he don't mind lies because when someone wants to hide something they have a clear goal: the desire to deceive; but that "fakes" that put on an act for no reason at all make he want to vomit referencing Shirou because until now that was what all his smiling was but since it wasn't his empty one, it makes it then thousand better than an act.
Shirou eventually gets out Miyu bringing her to go see her real family's graves in order to tell her the truth about her adoption but they are interrupted by Julian claiming that it was the most boring plot development ever. He then asks Erika Ainsworth if Miyu was the one without doubt, to which she responds by saying that the container was intact. Julian let out his rage by telling to Shirou what he has done to find the "thief" that stole what he was looking for, forcing Shirou to use Reinforcement on his tape measure to deal with him and tell Miyu run away. Julian proceeds to make Shirou fall with Flash Air from a certain height and immobilize Miyu. After learning that Julian was the one that caused the shadow that destroyed a part of Fuyuki and erased Miyu's family, he rushes to him but is stopped by Angelica Ainsworth who attacked him from behind with the power of her Archer Class Card.
He is saved by Kirei Kotomine, mistaking him at first for Kiritsugu after waking up. Kirei tells him that he is a priest that helps drowning people. After changing, he welcomes Shirou to the Fuyuki Church, presenting himself as a priest that is responsible for witnessing the end of the world. He mentions Miyu and Kiritsugu in order to keep Shirou in the Church. He proceeds the conversation by explaining to him the identity and goals of the Ainsworth family and the meaning behind the Holy Grail War, claiming that there has already been 4 rituals that ended in failure and revealing that had the worst outcome possible, destroying Zachary Ainsworth the previous head of the Ainsworth family, the Matou family and the Sakatsuki family completely. After the discussion, Kirei tells Shirou where MMiy was at the time they were talking, giving his details about the displacement field.
After struggling without success to reach the Ainsworth Residence and paying Kirei for Black Keys during this time, he meets with Sakura who was passing in front of his house. After eating with him, she reveals that she wanted to give him the Archer Class Card containing Gilgamesh's spirit to allow him to participate in the Holy Grail War but they are attacked by Shinji Matou who shows himself as the Card User of the Assassin Class Card. Chasing Shirou and Sakura to garden of the Emiya residence, Sakura decides to confront him with the Card to protect Shirou but it is revealed that the Card was a fake because the Ainsworth family knew that Sakura would betray them. Shinji then uses Zabaniya: Dead Heartbeat Melody to kill her, letting the card fall into Shirou's hands. Understanding Kiritsugu's words that on the road of trying to save everyone, there lies a cliff where one loses everything, he finishes by linking himself to the Archer Class Card and perform a Complete Install, cutting Shinji's right hand.
Shirou then fights a panicking and irritated Shinji who finishes by creating an empty decoy to sneak himself behind Shirou's back but is noticed by him and stabbed with Caladbolg II. After being defeated, Shinji says that he finally remembered everything and that he was already dead, asking Shirou to finish him off. Before dying he tells Shirou that he will have to kill a lot of people during the war and then leaves the Doll's body he was placed into. During the War Shirou faced Atrum Galliasta the Card User of Caster, Kariya Matou the Card User of Rider, Beatrice Flowerchild the Card User of Berserker, Kayneth El-Melloi Archibald the Card User of Lancer and Zachary Ainsworth the Card User of Saber. After collecting all the cards, Kirei comes to congratulate him on being the victor of the Holy Grail War and then tells him the location of where Miyu was.
Shirou meets again with Julian in the Ten no Sakazuki cavern of the Mount Enzou and asks him to give him Miyu back. After understanding what Julian has been through, he mentions that he knew someone like him referencing Kiritsugu but then explains to him what the Sakatsuki family was trying to do to protect their children. Shirou then shows his will by saying that if protecting Miyu was considered evil, then he would become an incarnation of evil. He then leaves Julian.
At the heart of the cavern Shirou finally reaches Miyu, who gets emotional because the Ainsworth revealed that Shirou and Kiritsugu took her with them only to use her as a tool. Shirou takes out the seven Class Cards and reaffirms to Miyu that he is an older brother and protecting his little sister is part of that. Shirou laments to Miyu about what he was trying to figure out to do and all his past actions had been one mistake after another, even the one he is about to make. Shirou proceeds to make his wish upon the Holy Grail, using it to send Miyu to another world, one where she could have happiness. While the Grail was working to grant his wish, Shirou is confronted by the wielder of the true Archer Class Card, Angelica.
Angelica assaults an unarmed Shirou with the Gate of Babylon, with the the swords only grazing him yet still enough force to throw Shirou off the ground. Angelica states
it was foolish of Shirou to fight her without a Class Card. She commands Shirou to stay down lest she kills him for real. He ignores this, and true to her words Angelica fires a second volley, this time for the kill. Shirou chants "Trace On" and projects Kanshou and Bakuya to deflect the incoming swords, much to Angelica's surprise and disbelief that her opponent could use a Heroic Spirit's weapons without a Card. Shirou explains every time his body fought with his Archer Class Card, he was being invaded by Heroic Spirit EMIYA. He projects several more swords, and mocks Angelica that she was slow on the uptake proclaiming she "is facing a true imitation of a Heroic Spirit". Shirou charges towards Angelica, exchanging sword fire, managing to reach her, but he is eventually pushed back. Angelica then belittles her opponent, labelling Shirou's power as a "trick". Understanding the true powers of Heroic Spirit EMIYA ("And then that Man..."), Shirou gets back up and utters the words "I am the bone of my sword..." . Angelica quickly retaliates with
Gate of Babylon but Shirou projects Rho Aias to shield himself. Angelica is forced to use Enkidu to trap Shirou in the process and charges at him with a giant sword. However, just before the attack is fully executed, Shirou casts his Reality Marble, avoiding the attack, and enclosing Angelica within his snow version of Unlimited Blade Works. The two continue their battle, however, it is soon clear to Angelica that through this world Shirou is not only able to keep up with but also nullify the Gate of Babylon. Angelica summons shields from the Gate to guard against her opponent's offense but Shirou smashes through the shields with his own giant sword. With his foe rendered defenseless Shirou goes in for the kill.
Shirou misses, as Angelica defends with Flash Air, and is subsequently teleported high above the ground, echoing what Julian did earlier. As Shirou is rendered helpless in the air, Angelica brings out Ig-Alima and Sul-sagana to crush Shirou but he quickly projects the respective imitations to counter the two Divine Constructs. After seeing her attack repelled and commenting about Shirou's "abhorrent self-destructive conviction", Angelica finally summons Ea to finish the fight. Realizing that it was impossible to reproduce this Noble Phantasm and that there is no sword in the world that can stand equal to it, Shirou, in a hopeless yet desparate attempt, musters every last sword stored in his Reality Marble and launches them against Angelica. Ea is activated, unleashing Enuma Elish, and the full might of Shirou and Angelica's powers collide. Although Ea's power proved overwhelming, Shirou managed to hold off Angelica's attack long enough for Miyu to leave their world. However, Miyu was transported along with everything in the surrounding area, which included everything related to the Holy Grail ritual in the cavern, but since Angelica and Shirou were in Unlimited Blade Works, they were not transported with Miyu to Illya's World. At that moment Shirou felt that a very important connection had been cut and finally realized that the one who kept him going was Miyu all along due to mana share. Shirou is wiped out by Enuma Elish, and is utterly defeated. Shirou affirms to Kiritsugu that though he failed to be a hero who could save others, for him he won because could pride himself as a brother who was able to protect his sister. Shirou collapses and is held captive by the Ainsworths thereafter.
Sixth Holy Grail War
At the start of Fate/kaleid liner PRISMA☆ILLYA 3rei!!, Shirou is first found by Illya, Tanaka, and Gilgamesh as they sneaked through the Ainsworth estate to rescue Miyu. As Tanaka notices that someone has been imprisoned, they first believe it to be Miyu until they heard his voice. Upon him questioning how they know Miyu, he is overjoyed to the point of tears after realizing she has made friends. Introducing himself as her older brother, Gilgamesh is excited that he is still being kept alive, although in a bad state, somehow having knowledge of his existence. He disparages himself for not being able to allow Miyu to escape the "chains of fate" after she has once again been brought back into the hands of the Ainsworths, begging them to save her.
Illya cheers him up by telling him that she will do her all to save her friend, causing him to once again weep as he claims that half of his wish has already come true thanks to her. He tells them to worry about Miyu instead of him, and they have no capability to open the magical lock of his prison before Angelica attacks them. Worried that she has returned, he tells them to run because she is dangerous. As Illya questions Angelica about Miyu's whereabouts, he tells her that she is at the top of the tallest tower, causing Angelica to use a spell to cause him great pain. Julian later threatens Miyu to take out any punishment that he cannot inflict on her body on her brother, causing her to become obedient for his ritual.
As part of their plan on their second assault of the estate to save both the captured Illya and Miyu, Kuro, Bazett, and Gilgamesh plan to rescue him to keep him from being used against Miyu. Gilgamesh also has some sort of motive in meeting him at least once, so he frees Shirou and tells him of the events until then. Once Julian uses the mysterious cube object to conjure a large number of Heroic Spirits, Shirou arrives as the rest of the combatants are overwhelmed and Julian is attempting to lure Miyu back to him by working at her conscience over her friends being in danger. Illya stops her by telling her nothing good would come of it, and Shirou agrees with her as he arrives.
He tells Miyu that she will no longer have to listen to Julian again, thanking all of her friends for fighting for her sake. He tells them to leave the rest to him to accomplish his duty as Miyu's older brother, crushing a number of the Heroic Spirits with Nine Lives. He tells Julian that he will accept "all the evil that comes with stopping him" if he is willing to sacrifice one person for the greater good. He asks Julian if he as enough resolve as a "hero of justice", and blocks a volley of arrows with Rho Aias. The members of Illya's group recognize him as Shirou, confused by his appearance. He projects Ig-Alima to act as a ramp to the formation where Julian resides, reuniting with Miyu on his way up. He apologizes for not being able to protect her, but states that he will end it all.
Encountering Angelica in Gilgamesh Install on the top, Shirou challenges her and tries to invoke Unlimited Blade Works, but his body failed him due to his poor condition at the time. After Angelica cornered him, Kuro comes to his support and together they defeat Angelica. But on the way to Julian, a doll of Sakura Matou from Miyu's world in install form attacked him, countering his projected weapons with Knight of Honor. Defeated, Beatrice Flowerchild tosses him from Ig-Alima where Rin Tohsaka saved him.
He attempts to save Illya and Miyu from a blast from Thor's hammer by using Rho Aias, which nearly resulted in his death due to the damage he had suffered from battle and the wounds healed by Tohsaka re-opening. In a way similar to his Stay Night counterpart, he is healed by Tohsaka.
After being saved from death and with the battle over, the still wounded Shirou leads Illya and her friends away from the crater and back into town. Finding out they have no place to stay now that their base at the school has been compromised, Shirou invites them to the Emiya Manor, including Angelica Ainsworth who had been abandoned by the other Ainsworths. Arriving, he welcomes Miyu home and allows the rest to use his home and the clothes they have available. Later, after bathing and bringing Tanaka home from the school, Illya and Chloe eavesdrop into a conversation between Miyu and Shirou. There Shirou dotes on his little sister, showering her with kind affection, even doing her hair up. When Miyu tells Shirou about Illya as her friend, Shirou thinks to himself how grateful he is his wish was granted.
Embarrassing Miyu by revealing the eavesdropping, he informs the trio to gather the rest of their party in the main room. Once all gathered, Shirou expresses his sincere gratitude to them all and tells them the story of the Fifth Holy Grail, the betrayal of his only friend, and the cost of his victory.
During the group's recovery over the next few days, Shirou meets with Chloe privately to give her Kiritsugu's Thompson Contender and the remaining magus killer bullets. He does so, knowing he will not be able to be healed enough to aid them in their fight against Julian.
Shirou uses Projection with great efficiency. He is able to run through a field of Heroic Spirits that leaves the members of Illya's group easily pushed back, attacking and defending as he moves. He is able to project a Divine Construct, Ig-Alima, for which even Gilgamesh praises him despite it being a hollow knockoff of the real weapon.
His sword skills are also worth noting, as he seems to employ a fighting style similar to that of Archer's; a dual wielding style that allows him to fight against far stronger and faster opponents by usage of various tactics and exploiting every detail about his opponent's abilities.
This iteration of Shirou is also capable of evoking a variant of Unlimited Blade Works which is covered in snow.
He was the user of the Archer Class Card before it came to the hands of Illya, and displays control over it to the degree of reaching a Complete Install. He is shown to have greater experience than an actual user of it, such as Kuro, as she's stated to learn how to best use the card's powers after watching Shirou fight.
Just like the Heaven's Feel iteration of Shirou, this Shirou has showcased to have been affected by the Archer Class Card. As a result, the more he uses his projection powers which "doesn't belong to him", the more he gets consumed by the powers, effectively turning him into a younger version of Archer, as displayed by tanned skin and strands of white hair. It is also worth mentioning that unlike his other selves, Kiritsugu trained him properly and he can reinforce objects perfectly. Due to having the EMIYA heroic spirit possess him, he shows many times he has acquired somewhat super human attributes such as his immense strength and agility as well as a somewhat abnormal degree of healing though it is limited to cuts and broken limbs.
 Fate/side material - Encyclopedia: Magic Circuits [Magecraft], p.073 [T]
Magic Circuits [Magecraft]
Pseudo-nerves within the body of a magus.
Magic circuits are responsible for converting life force into magical energy, and for connecting to the underlying grand sorcery formula.
Because the number of magic circuits a person has is fixed at birth, magi lineages do what they can to improve themselves and create an heir with even one more magic circuit.
Once the magic circuits have been opened for the first time, the practitioner can switch them on and off at will.
Each practitioner visualizes the flipping of this switch in their own particular way. For Shirou, the image is that of a gun's firing hammer, while for Rin it is stabbing a heart with a knife.
This image tends to be related to how the circuits were opened for the very first time, so there even those who can only open their circuits through sexual arousal or self-harm.
By the way, Shirou's number of magic circuits is an unexpectedly high 27.
Rin, on the other hand, has 40 main circuits, while her sub-circuits are 30 each.
- PRISMA material/pre - minor translation by zikari8
- Fate/kaleid liner PRISMA☆ILLYA 3rei!! - Chapter 22.2: "One Hand Takes, Another Hand Saves"
- Fate/kaleid liner PRISMA☆ILLYA 3rei!! - Chapter 27: "Persevering Miracle"
- Fate/kaleid liner PRISMA☆ILLYA 3rei!! - Chapter 28: "The Siblings' Home"