Shirou Emiya

Shirou Emiya (衛宮 士郎) is the protagonist of Fate/stay night who acts the Master of Saber during the Fifth Holy Grail War. He is an unorthodox magus who makes use of a very specialized version of Projection magecraft. He has made it his goal to become an Ally of Justice (正義の味方) who will save everyone regardless of what happens to his own life.

Background
Ten years before the start of Fate/stay night, Shirou was an ordinary boy living with his parents in Shinto. The great fire caused by the wish of Kotomine at the end of Fourth Holy Grail War killed both his parents and left him mortally wounded within the blaze. He was rescued by Kiritsugu Emiya , who was dejected after the events of the war, and wishing to atone for all of his actions, he saved Shirou's life by embedding Avalon in his body. He then later asked the recovering Shirou if he would like to become his adopted son, fully disclosing his identity as a magus. Shirou agreed and spent the next two years persistently asking Kiritsugu to teach him Magecraft. Kiritsugu eventually complied, and though he disapproved of Shirou's desire to learn his craft, he advised applying it in secret, where it could only benefit people and not attract confusion or suspicion. The knowledge he imparted on Shirou was very basic and incomplete, leading him down a dangerous path with little results. Furthermore, and perhaps inadvertently, Kiritsugu passed on his philosophy of wishing to be an Ally of Justice capable of saving anyone to Shirou.

Five years prior to the fifth Holy Grail War, Kiritsugu suddenly died, leaving Shirou frustrated, depressed, and alone. He was subsequently watched over by Taiga Fujimura, Shirou's longtime neighbour and his English teacher, and his living expenses were managed by her grandfather, Raiga Fujimura. He later went to a middle school where he encountered Matou Shinji around October of his second year when he had to remake the signboard of the culture festival according to the design of third year students in a single evening. Shinji, who oversaw that throughout the evening, said “Hmm… you’re an idiot but actually does a pretty good job.” and started to laugh.

After starting in Homurahara School, he met Issei Ryuudou and became known as someone who would readily do anything to help others, such as fixing the school equipment. He later joined the Archery Club, which led to an estranged relationship with Shinji. He missed the target only once during the period that he was enrolled, but even then he said that he saw that “it will miss” before even shooting it. He withdrew during the summer of his first year due to a bone fracture in his right shoulder he received during his part-time job, which left a burn mark over the skin. The wound itself was nothing major, but Shinji pointed out that it was unsightly for someone with a burn mark to do a formal shooting, so he left the club as it was also a period when he was busy with his part-time job. Their relationship eventually stabilized, but some tension still remained, especially in regard to Shinji's abuse of Sakura. Shirou also got closer to Sakura, as she started to visit his household frequently during the period while he was injured in order to help him cook and clean up the house. Even after he was healed, she continued to come as a member of his surrogate family.

Hobbies
Shirou possesses an extraordinary talent for housework. Despite having Taiga as his caretaker, he generally provides for all of her meals and does almost all of the housework, whereas she generally does nothing. Home cooking is his forte, and he especially prides himself in Japanese cuisine. He is not a cheapskate when it comes to ingredients to make a delicious meal, and he will spend a great deal of time in order to make something extravagant. He teaches Sakura how to cook, and as she improves, they eventually start to compete over the quality of their meals. Shirou equally enjoys Japanese tea, black tea, and coffee, but he is better with Japanese tea, and he dislikes plum kelp tea. There are times when he receives liquor from Copenhagen, but he merely tastes it as he is not good with alcohol. Among the characters of Fate, he is one of the heaviest eaters, losing only to Saber, Berserker, and Lancer. According to him “one who does not have the stomach to digest breakfast is a failure as a martial artist.” Despite having his household finances taken care of by Taiga, Shirou doesn't wish to feel like a freeloader, so he has been taking up part time jobs since middle school in order to pay for his own expenses. He earns 950 yen per hour at Copenhagen, and he recieves spending money from accompanying Raiga Fujimura when he participates in his hobbies, which include sumo wrestling and hunting.

Shirou does not feel good in the atmosphere of a Game Center. He is weak against blind dates, even though he likes them. He has never gone to the dentist. His English is poor and his intended major is initially in the field of law and politics. He likes repairing electronics to help practice his Magecraft, and he can become immersed for hours at a time while fixing appliances. Due to the fact that he almost never denies requests to repair appliances or work, such as cleaning the school's swimming pool before its opening, he has many nicknames such as “fake school janitor”, “in charge of mending”, “vacuum cleaner of the Archery Club” and “Homurahara’s brownie”. He likes to meditate within the dojo in his household, often to relax before or after practicing Magecraft.

While at school, he aims to be the greatest at the “who will give up first” type of contest. He once participated in sepak takraw along with Ryuudou Issei and Matou Shinji during a school festival. They advanced to the finals, but when they competed with the team formed by Kane Himuro, Ayaka Sajyou and Ayako Mitsuzuri, Issei caused a quarrel after being harassed with concentrated attacks and made both teams be disqualified.

Personality
Due to the trauma suffered during the great fire, Shirou has a constant emptiness in his personality. He feels that as the only survivor that it is unfair to the deceased to prioritize his own needs before those of others. He has a distorted sense of values where he finds self-worth from helping people without any compensation, feeling that the very act “helping people” is its own reward. When it comes down to receiving an injury or even giving up his life to help someone, he will do it without a second thought. The people who see this side of him are often very worried and attempt to correct his behavior, though they are unable to change his opinions. Kiritsugu often talked about how he used strive to protect the innocent from the world's many perils, even at the cost of his own humanity, and how he was saddened by the reality that whenever he was able to spare one life, another person was fated to die. Although Kiritsugu was tormented by his inability to save everyone, Shirou always admired his efforts. Right before Kiritsugu's death, Shirou pledged to be an "Ally of Justice" in Kiritsugu's place and strive to protect everyone at the cost of his own life.

Shirou takes his ideals to the limit during the Fate scenario, where he constantly attempts to protect Saber from harm and keep her from fighting other Servants, despite the fact that she is many times more powerful than he. This is because he cannot stand the idea of someone else being harmed for his sake. He never gives up his ideals during the route and injures himself numerous times to uphold it. During the Unlimited Blade Works route, Shirou, through constant arguing with Archer, begins to see the hypocrisy in his ideals. Though he refuses to give them up entirely, he works his way towards a middle ground where he will strive towards fulfilling ideals, despite knowing they are impossible to achieve. He faces his largest dilemma during Heaven's Feel, where he is forced to choose between maintaining his ideals and protecting the life of Sakura. He eventually forsakes them, with the exception of the "Superhero" ending, where he becomes as resolute as Kiritsugu in his prime, allowing Sakura to be executed for the greater good. He strives only to protect Sakura, though he is presented with conflict a number of times.

Shirou is extremely stubborn once he sets out to accomplish something, such as spending hours attempting to perform a high jump that is nearly impossible for him. This action, as watched by Rin and Sakura, is one of the initial factors that causes them both to develop feelings for Shirou. He will stubbornly defend his own viewpoints, no matter how wrong they may seem to others, even to the point of causing them great mental anguish. Though he does his best to help others, if he feels that a person brought about their own ruin, he will simply watch instead of helping. Nasu has stated that Shirou and Shiki Tohno would definitely get along badly.

Fate/Zero
He appears near the end of the story. He lost his family to the great fire of the grail, as he laid on the floor trying to reach out to someone. Kiritsugu found him and thanked him who happily cries in tears.

After being rescued by Kiritsugu from the inferno he is adopted as his son. Shirou felt comfortable calling Kiritsugu as Old-man (Jii-san) than Father or dad.

In the Drama CD, Shirou kept experiencing nightmares. Shirou would take the medicine that Kiritsugu made with magecraft. Shirou asks Kiritsugu about teaching him magecraft but Kiritsugu was completely against it.

Later while gazing at the stars in the Emiya estate Kiritsugu tells Shirou of his dream to be an Ally of Justice and how he failed. Shirou in admiration states he will achieve Kiritsugu's goal and this allows Kiritsugu to pass away peacefully.

Fate/stay night
See Main Route Articles for Shirou's role during the scenarios: Fate, Unlimited Blade Works and Heaven's Feel

Shirou is a Student of Year 2 Class C of Homurahara School during Fate/stay night. He has no interest in the Holy Grail, and instead despises its use. However, he is determined to win the Holy Grail War with Saber for he hopes his efforts will ensure that another disaster like the Fuyuki conflagration will never occur again.



In Heaven's Feel, Shirou's body was completely dead to the point that even the Holy Grail could not restore it, but Illyasviel von Einzbern resurrected his soul with an imperfect Third Magic and revived him by giving him nothing else but a basic body. This is not like pouring a spiritual body and consciousness into the brain of another to manipulate it, but a materialized soul that possess human functions which was given a body by the Third Magic. By giving a body to the soul, the flesh is perfectly reproduced after the shape of the soul. However, because Illyasviel's Third Magic was imperfect it took half a year of continuous trial and error, but in the end a basic body made by Touko Aozaki was purchased with the money from selling the books of the Matou family to the Mage’s Association and things were settled for the time being.

But even in this state where the soul operates the body by remote control while remaining inviolable in the other world, it still does not mean that he is immortal, as he can grow old, still has a lifespan and will die if grievously wounded. Nonetheless the soul cannot remain in this world without the body, because instead of the soul reproducing the body that is dwelling in, it is being fixed by that body. In short it is a like the state of a dead Servant that can take action without a Master and is living in the same way as a human being.

However, because Touko Aozaki had less Magic Circuits than Shirou, the transference of prana is bad. It seems that in this state, the strong point about Shirou’s basic body is that because it was repainted by the soul the original one became ordinary, but the flaws of the original were retained as they were.

Manga
The manga adaptation of the visual novel follows the Fate route with a mixture of events from Unlimited Blade Works. It follows the events of Fate normally until the defeat of Rider. Instead of Shirou being immediately kidnapped by Ilya while Saber is weakened, Saber manages to recover somewhat from her use of Excalibur before the Emiya household is assaulted by Caster. Using Taiga as a hostage, Caster successfully uses Rule Breaker on Saber and takes her as her Servant after Shirou was unable to make a quick decision. When Rin tells Shirou that he is no longer a master and should not be involved any further, Shirou becomes depressed and becomes confused with what to do (noted: Shirou's feelings for Saber continue to develop).

Feeling depressed over his loss and worried over Saber, Shirou goes to the Church for shelter. At the, Church Kotomine tells Shirou that his decision to sacrifice Saber was the right choice. Enraged, hearing such a thing Shirou counters Kotomine, saying that that (sacrifice Saber) was wrong and that he never truly gave her up. Kotomine then counters Shirou saying that not accepting what he did was the real betrayal. Kotomine then reveals to Shirou that his father Emiya Kiritsugu was also a Master in the Holy Grail Wars and that he was the victor. Shirou was both shocked and horrified even further after being told the truth. Kotomine tells Shirou that Kiritsugu was the man who kill all the other masters and caused Kotomine's first death in order to attain the Grail, and making Shirou believe that Kiritsugu was the one responsible for the huge fire that, killed so many people ten years ago (although this is only half true, as Kotomine was the one who made the wish to make everyone in the area disappear). Following, this Shirou begins to have visions of Saber thanks to his mental link with her. Shirou then decides to come out of hiding and rescue Saber. Kotomine, then acknowledges Shirou as Kiritsugu's son and secretly swears to end Shirou's life personally.

Shirou tracks down Caster and Kuzuki only to be beaten by Rin and Archer. During the battle while Rin attempts to reach Kuzuki, and Caster overwhelms Archer until she temporarily retreats upon Archer starting to unleash Unlimited Blade Works. Kuzuki bringing a defeated Rin stops the battle, and Archer is forced to also become Caster's Servant in exchange for Rin's safety. Caster reneges on the promise by ordering Saber to slay Rin, but Shirou saves Rin and takes her to safety just in time.

After the loss of Archer, Shirou and Rin are approached by Lancer, who has come to offer some help. They attack Caster and Kuzuki who have taken over the Church. while initially overwhelmed, Archer, having been waiting for his chance to kill Caster, assassinates both her and Kuzuki before turning his attention to Shirou. Shirou who has become disgusted with Archer, engages Archer demanding why Archer hates him so much, The two are stopped by Rin who manages to convince Archer from killing Shirou by talking it out. Rather than Rin forming a contract with Saber, Shirou manages to become her Master again, while Rin becomes Archer's Master again. It continues to follow the Fate route afterward, Shirou's feelings for Saber continue to develop and her for him as well.

Fate/hollow ataraxia
As of the setting of the game, set half a year after the end of Fate/stay night, Shirou has successfully graduated to Year 3 Class C of his school.

The Shirou present in the game turns out to be a facet of the illusion created by Avenger to satisfy Bazett's wish to keep on living. Avenger takes on Shirou's persona during the daytime of the four-day temporal loop, where he has no knowledge of his existence as Avenger. He explains it as Avenger himself equaling "zero", and no matter how much "zero" is added to "one", it still only equals "one." As Shirou, he comes to care for other people, especially the mysterious Caren Ortensia. Eventually, Shirou realizes the existence of the temporal loop, which leads to him attempt to resolve it. The main problem is that Avenger enjoys his daily life as Shirou so much that he doesn't wish for it to end. Caren, who Shirou never meets due to dying whenever they come across each other, reveals to Shirou and Avenger that they are one and the same, and that he is the cause of the loop. Much to Bazett's sorrow, Avenger decides to put an end to the loop and returns to the void of the Grail.

The real Shirou only appears in the prologue, during the part where Rin is telling horror stories in Ryuddou Temple and in the epilogue, when he is visited by Bazett and asks him if she can stay living for a time in Emiya's residence, which was the first time that they meet. Shirou also know of Caren before the events of Fate/hollow ataraxia.

Fate/unlimited codes
He is given the title Apprentice Mage (見習い魔術師) in Fate/unlimited codes.

Carnival Phantasm
In Episode 1, he participates in the Holy Grail Show alongside Saber and wins. However, after that, he is dragged by several Neco-Arcs to a rocket, which launches far away. By the time of Episode 2, the rocket fell on a beach (where are the Tsukihime characters) as he and Neco Arc are seen trying to repair it. In Episode 4, he and Shiki Tohno meet and discuss their problems namely how they can accomplish dating all the girls of their respective series on the same day. Shirou wants to date them all because he wants to make them happy. After that, he makes small appearances.

In Episode 9, he and Saber compete at the Grail Prix, in which they use a lion riding toy to insert coins in it called "Unit Lion". While at first they seem to be losing, because the car needs coins to work, in the end they manage to win by inserting in the car all the money that was for lunch. After winning the Grail, Shirou and Saber wish to have back their lunch money. In Episode 12, Shirou uses Shiki's plan to date Saber, Rin and Sakura at the same time, but fails miserably and he is punished by an angry Saber. He finally appears at the Ahnenerbe party, discussing with Shiki and Mikiya Kokutou the possibilities of a new season.

Combat
Shirou is initially completely inept as a magus, only able to use Reinforcement and Projection Magecraft with a low level of success. Reinforcement allows him to analyze the structural composition of an object, and increase its effectiveness, such as making it more durable or its shape more practical, or return it to its original state. He can also use it to improve upon the physical capabilities of his own body, such as his eyesight, allowing him to see as far as four kilometers away. Shirou is also very skilled in Structural Grasp Magecraft, which allows him to understand the structure and design of objects as if he were viewing a blueprint. Projection, while a high level skill, is generally considered useless compared to Reinforcement due to the higher prana cost, and anything that Shirou initially projects is useless and hollow. Though the objects merely imitate the shape, there are only a few who can identify them as fakes in a first glance. Any practitioner that analyzes composition wouldn't be able to see through them, and even one that works through spiritual mediums would only notice a sense of incongruence. Since only objects with history ever go into the Department of Spiritual Invocation of Clock Tower, there is a low probability of them being discovered.

Shirou is later capable of using Tracing, a higher level version of Projection that completely copies everything regarding the creation and existence of the object. During the Fate scenario, he slowly learns of it on his own by training with Rin and following Archer's advice: "If you can't defeat it, then imagine what can", while in the Unlimited Blade Works scenario, he learns of it through extensive contact with Archer. He is only effectively able to reproduce swords, other weapons, and armor, but this specialty allows him to faithfully reproduce even legendary weapons. He is capable of reproducing any sword that he has seen, though Noble Phantasms are always one rank below their original strength and armor costs three times the amount of prana, and he is capable of employing its entire history, allowing him to wield any weapon with the same proficiency of its original owner. He has to see the weapons with his own eyes to reproduce them, as even the blueprint of Zelretch is not enough to reproduce it, but by seeing it and Caliburn through shared memories of Justeaze Lizrich von Einzbern and Saber, he becomes able to fully trace them afterward. If the weapon is not made of materials that exist in the world, such as Ea, he cannot analyze or reproduce it, though he can tell its basic nature. He is also quite capable of creating his own original kinds of weapons, should he put his mind to it.

It is later identified that these abilities and Shirou's affinity with swords are concepts of Shirou's Reality Marble, Unlimited Blade Works. Rather than simply creating his projections in the real world, he actually reproduces them within the Reality Marble, as if he were loading a gun, and then projects them into the real world as if he were firing it. This allows him to prepare dozens of swords at a time for later use. Shirou is unable to properly deploy or maintain Unlimited Blade Works due to a shortage of prana, but with a proper contract with a magus with a suitable level of prana, such as Rin, he is capable of using it. If he were to learn about it normally, unlike the situation in Unlimited Blade Works where he learns of it firsthand from Archer, it would take ten years of training to set the foundations for the ability and another ten years to reach to the point of being able to use it. While actually using Unlimited Blade Works, the cost for creating the weapons is greatly diminished and the speed at which they can be created is also increased, allowing him to easily overwhelm Gilgamesh and his Gate of Babylon.

If Shirou were to fight Shiki Tohno, there would be a high probability of a mutual defeat where Shirou would have his projected Noble Phantasms one-sidedly killed, while Shiki would overuse his Mystic Eyes of Death Perception to the point were he would overload and self-destruct after the battle. Circumstances would change if Shirou were capable of an Excalibur-like prana discharge. During a fight with Bazett Fraga McRemitz, a professional that specializes in anti-magus combat, he would likely be overwhelmed by her techniques, experience, and tactics, and he would also constantly have the disadvantage that using any of his high level techniques would leave him susceptible to Fragarach's instant kill ability.

Knowledge
Shirou's basic training in Magecraft was extremely lacking, so he was left with the idea that he needs to create a new Magic Circuit with each use of Magecraft. He goes through extremely dangerous training, which he describes as the feeling of inserting a hot iron rod into his spine, where he constantly faces the risk of death in order to develop a new Circuit. Though his body has twenty-seven natural Magic Circuits, they had been abandoned for his nerves, which he made into makeshift Magic Circuits due to his wrong method of training. Once his real Circuits are awakened, he goes through extreme pain and suffering as his nervous system gets used to the new intake of energy. His newly opened Magic Circuits can barely handle ten units of prana each. Shirou will never leave the level of a magus apprentice, compared to Rin classified as a "100", Shirou would be a "10", but as a specialist spellcaster, he would be received as someone on par with Kiritsugu’s evaluation as a “Magus Killer”, where he would be classified as a "40" compared to Rin's "100."

Shirou has Avalon implanted within his body, which saved his life during the great fire. This gives him an extremely potent regenerative ability while Saber is summoned due to Excalibur, though it does seem to sustain him even without it as he was able to temporarily survive a fatal blow dealt by Lancer. This allows him to survive numerous fatal wounds though it works against him in bad endings where he is able to be tortured and mutilated without succumbing to his injuries for a long duration of time. Unlimited Blade Works also seems to protect Shirou by creating blades within his body to reinforce it. He is able to survive a blow to the chest from Rider's dagger, which is repelled as if it is hitting metal, a kick that would have gouged his stomach only knocks him away, and he manages to keep from having his entire body destroyed from an attack by Gilgamesh. The ability seems to go out of control during a bad ending where numerous swords sprout from his dying body, and while his body is fully breaking down in the Heaven's Feel scenario, they are constantly being created and protruding from his skin. He practices basic swordfighting with Saber, though it amounts to little in actual offensive capabilities. While she teaches him, he cannot use her fighting style as a model. He cannot see exactly how she is attacking and their different physiques makes her impossible to copy.

Fate
During Fate, Shirou only learns the basics of his abilities, leading him to only trace Caliburn and Avalon.

Contradiction
Shirou and Archer's connection is a large part of his development in the Unlimited Blade Works route. The contradiction of Shirou Emiya and the Heroic Spirit EMIYA existing at once is much like magecraft that allows one to acquire skills from the past by possessing themselves with a previous self. The more they come into contact, the more of his knowledge and techniques flow into him. The abilities suit him perfectly, as they are Shirou Emiya's optimal technique, perfected over many years of training.

It is first noticed after several training sessions with Saber, when he makes a drastic improvement over the previous day. Copying Archer's technique, he begins to make less unnecessary movements, allowing him to desperately avoid her counter-attacks rather than become instantly knocked out, and as his body is already fit, just the knowledge of proper techniques can improve his fighting quickly.

He is captivated by Kanshou and Bakuya, and uses it as a basis for a two-sword fighting style. He doesn't have a basic style, so it is immediately evident that he is copying Archer. The flow of it is so unconscious that he believes that Saber is going easier on him, and his sword is able to automatically parry her strikes even though his body cannot react to them.

The effect greatly magnifies after they recognize each other's identities, causing extreme pain as it flows into him. His body begins to break every time they touch, as he has learned too much of his future self while trying to match him in skill. He even begins to obtain Archer's memories, such as the reason behind his hatred for their shared ideals.

Projection
Once he learn the true use of Projection, he lacks proper training so even the most basic projections cause him pain and the majority of the swords generated shatter upon impact due to their low quality. He projects both Archer's sword technique and his reproduction ability, but it is flawed because he doesn't understand that they originate from his Reality Marble. Unlimited Blade Works cannot be utilized without that realization, and even after coming to that conclusion, he does not have the necessary energy to utilize it on his own.

He forms a contract with Rin to have her provide the necessary prana to form his Reality Marble and he manages to project a number of weapons from the Gate of Babylon in order to defeat Gilgamesh.

Archer's arm
Shirou does not develop his abilities as he does in the other routes during Heaven's Feel. He uses his basic Reinforcement magecraft on a stick and wooden sword during the early part of the war without grasping onto Projection. During the first conflict in the Einzbern Forest, he loses his arm while protecting Ilya from the Shadow's explosion. The wound is fatal, so Archer, having also suffered a fatal wound, tells them to transplant his left arm onto Shirou. Attaching a spiritual body to a normal human body requires a spiritual doctor like Kotomine because the process it more akin to healing the soul rather than the body.

Kotomine manages to attach Archer's arm (アーチャーの腕) to replace Shirou's lost arm. It is a "foreign substance" that should not be there, attached by opposing the natural Providence, and joining two separate spiritual bodies is forbidden magic that cannot normally succeed. The formation of spiritual bodies deals with resurrection and restoration of souls, divine mysteries that cannot be handled with magecraft, so it would normally be that the recipient would die of shock even if the operation was a success in shape. Kotomine expected the completion of the surgery to result in his death, but Archer and Shirou being the same person makes them an exception to the normal rejection. Not knowing of their exact connection, he states that they are suited for each other and not even two twins would be more similar.

While the arm would have disappeared had Archer faded away while the surgery was in progress, it is now anchored to Shirou and can be called his own limb. Due to being transplanted while Archer was still in the world, it is part of a Heroic Spirit that has been connected to his Magic Circuits, and stays in the world using his own prana. While unconscious, the arm grants him knowledge on Archer, the basis of Projection magecraft, battle experience, and battle information. The sensation feels like his body is burning while countless ants enter the hole in his shoulder that is now sealed with flesh that isn't his own. While the sensation tells him to manage these skills, the level of information and power required feel impossible to him. Even if it becomes familiar with his body, he neither has the skills to handle it or the power to use it without destroying his body.

While they are the same person with compatible Magic Circuits, the power of the arm of a Heroic Spirit is not something a human can handle. No matter how suited he is to the arm, he cannot use its abilities without it eventually swallowing him due to his body being spiritually far inferior to the arm. It can be considered a weapon more than an arm, and it is referred to as an Artificial Phantasm in the scene's title. It passively flows Archer's battle experience and physical abilities into Shirou even while inactive. It acts like an overdose of strength-enhancing drugs, letting him demonstrate abilities beyond his limits.

He becomes able to easily leap out of the third story window of the Einzbern Castle, compared to around eight stories for a normal building, with only temporary numbness and pain upon landing. Unable to strengthen his body, he does bring a large amount of prana to his feet to lessen the impact and believes that landing on asphalt instead of grass would have broken his legs. Ilya mentions that Archer is influencing both his mind and body, making him think that he can easily handle the drop like Archer and toughening his body enough to survive. He can also run fifty kilometers per hour through the uneven terrain of the Einzbern Forest.

Shroud of Martin
In order to counteract the effects of the arm, Shirou is given a Holy Shroud, the Shroud of Martin (マルティーンの聖骸布), by Kotomine, as a seal which keeps Archer's circuits from connecting to his body because it has the ability to seal a certain event or return it to normal. It completely wraps around his arm with the exception of his fingers, and while it is initially completely numb, it eventually regains enough functionality after familiarizing with his body to allow him to lead an ordinary life. It would be possible to cut it off, but that would remove his only possible weapon in defeating Zouken.

The arm is treated as a different object even if he uses magecraft, but prana still constantly flows through the body even if magecraft isn't being used. Despite the Shroud cutting off the Magic Circuits, he will feel a great deal of pain if he doesn't concentrate to form a "barrier" to keep the "foreign substance" out of his unstable body when the arm reacts to the energy and tries to activate. It is easy to do once he figures out where the pain is coming from, and he is able to control it to an extent. Living with it is not quite as easy as Kotomine suggests because the arm randomly flows magical energy into his body. It constantly becomes hotter each time he moves it, and when it overheats, it sends the excess to the rest of his body.

While it first feels like he is being burned, he realizes it is more like he is being cut and stabbed by his own body. Simply undoing part of the binding for even a brief moment causes him to completely lose himself as his nerves and senses are overwhelmed by extreme pain and the feeling of impending death. He rambles on in his mind about how he is feeling more pain than ever before, "sitting on a mountain of swords", and that he can see all of his cells crumbling apart. He regains his senses a few seconds afterward, and he cannot remember the exact happenings during that period. He is able to manage at times, but also suffers a great deal of pain in intervals to the point of wishing to simply cut it off, or even risk removing the shroud to stop the pain. Its existence brings him true fear of an unavoidable death and utter obliteration, making it the first he has felt such since the fire ten years before. His ability to suppress the infringement from the arm even with the Shroud is limited to a certain extent. Kotomine believes that the arm will consume him within ten years, but it is possible for him to live to an old age if he trains to become a magus worthy of matching the arm in order to seal it without the Shroud. It is not an imminent threat, so he would have enough time to attempt do so if he wished.

Rin also shares part of her Magic Crest with him as a Warding Sign. She is able to transplant a small part of her Crest by placing her left hand on his body, comprehending it, and sharing her warding crest. While she was planning on giving him the capability to use a "switch" for his Magic Circuit, being able to turn it on and off is too dangerous in his current state. She instead performs it to suppress the magical energy by placing needles in his left shoulder, belly button, and throat so that the arm won't be connected to him unless he wishes for it. It also grants a resistance to magical energy, so that something that passively absorbs energy like the Shadow will have less of an effect on him. Her crest cannot familiarize itself with someone not from the Tohsaka family, so it is a makeshift that won't even last a week.

Projection
Shirou is currently observing Archer's magecraft rather than Shirou's magecraft, so he cannot use Projection in his current state without invoking the abilities of the arm. Ilya states that he will eventually obtain his own usage of Projection magecraft, but it is still only a possibility at his current level. His own Projection is still at the level where it will fail constantly due to his misunderstandings, but drawing on Archer's knowledge without invoking the arm can force him to "level up" quickly. He can loosen the Shroud slightly in order to practice retrieving Archer's knowledge without breaking the seal and only getting a small reaction.

With help from Rin's Magic Crest to increase his Magic Resistance and Ilya to protect his consciousness, he is able to experience Archer's Projection by interacting with the arm like opening a Magic Circuit. The knowledge is like poison, but the arm will continuously flow its experience into him. It is similar to pouring one hundred units of fuel into a container that can only hold ten, and he will likely only gain from less than a tenth of the agony he will endure. The knowledge disrupts his memories and leaves him with a large blank space after replacing the Shroud.

Projecting directly with Archer's abilities requires the removal of the Shroud, and while he may be able to recall the activation spell gained from Archer's knowledge, it would destroy his body to attempt using it. It can easily be removed at any time for instant access to the full extent of Archer's power. It is not something that lessens his life with each use, but the activation of a time bomb that will ultimately lead to his death the second he removes the Shroud. Archer's Magic Circuits will be activated if he uses the arm even once, and while he may last while using its abilities, his body will break down due to being unable to withstand Archer's magic. He will eventually be consumed, or more correctly "blown away", by the arm after the first activation.

Once it is removed, Shirou instantly gains access to Archer's Magic Circuits, battle experience, and techniques, but he cannot deploy Unlimited Blade Works due to the drastic change in his own inner world by giving up on his ideal of being an Ally of Justice. His Projection magecraft allows him to match Servants in direct combat for a limited time and even defeat them. He is able to trace "Nine Lives" to kill Black Berserker nine times with a single maneuver called "Nine Lives Blade Works" and later defeat Saber Alter with the Overedge technique of Kanshou and Bakuya at the cost of his mind during a bad ending. Using these abilities comes with a heavy penalty as Archer's circuits overload Shirou's body leading to his mind slowly eroding, the decay of his memories, and eventual death as his body and soul break down from being invaded by Archer's Unlimited Blade Works.

Puppet body
Due to Archer's arm and his overuse of Projection, his Magic Circuit is broken into pieces, and his death is one that even the Holy Grail couldn't reverse. He is resurrected by Ilya's imperfect usage of the Third Magic, reviving his soul and giving him a body free of wounds by preserving his soul and inserting it into a container. It would normally be that giving the soul a container or body would allow it to take perfect form by utilizing the "genes of the soul" rather than those of the body. His body is reconstructed from a portion of Ilya's body, which she mentions is a bit cheap as a container, so it is nowhere near his original form in terms of size. Its shape afterward is not that of a human, but as he mentions reaching his hands out and grasping onto Rin's pendant, it is at least vaguely humanoid. He is able to be found due to Rider using the pendant as a landmark to locate him, and while his exact form is left unknown, it is small enough to be "plucked" from the river by Rider.

He is not a true product of the Third Magic, a high-dimensional planar being, but it instead reanchors his soul to a vessel. They decide to experiment with various ideas for a proper body during the first six months, as he cannot simply grow in his current state. They do not have the resources to make a homunculus body, so they instead sell the books of the Matou household to obtain a puppet body left by Touko Aozaki. He is perfectly human even in this state, but Rin notes his soul is actually remotely controlling the body. He can receive surgery at hospitals, drink cold medicines, be killed, and eventually grow old and die of old age. The soul is fixed to the body, so he can be likened to a Servant that can operate without a Master.

He has some issues because body is used, but even other good puppet makers cannot match up to it. Rin wishes to find and consult Touko about it, but her Sealing Designation makes that a hard prospect. The prana doesn't flow well, but Shirou is fine with it because all other aspects are better than his original body. The soul will overwrite the body no matter its quality, so there will likely always be places that won't function properly. Sakura supplements his very weak Magic Circuit with her own overflowing amount in order to keep him from returning to his prior state. Despite the setbacks, Rin believes that he should be able to utilize Unlimited Blade Works with training, and that his being a successful example of the Third Magic is an extraordinary trait in itself.