Fate/stay night chronicles a two-week period in the life of Shirō Emiya, an amateur mechanic who attends school called Homurabara Gakuen in Fuyuki City. Ten years ago, Shirō was caught in a massive fire hazard that incinerated his parents and consumed a large portion of the city; as he was dying, an enigmatic man discovers and treats him. This man, Kiritsugu Emiya, decides to adopt him, though the two maintain a distant relationship because of Kiritsugu's frequent departures from Fuyuki City. One moonlit night, Kiritsugu and Shirō had a discussion outside of their home, and Shirō discovers a fact about his father that Kiritsugu was actually a mage.

“ I have a secret that I haven't told you--- I'm a Magi. ”

Through their conversation, Shirō learns of his foster father's failed life ambition to become a "Hero of Justice" (正義の味方, Seigi no Mikata?), a guardian of mankind who could protect the weak and innocent. Touched by Kiritsugu's conviction, Shirō affirms to his foster father that he intends to devote his life to achieving that distant ideal, much to Kiritsugu's chagrin. To do this, Shirō pleads with a begrudging Kiritsugu to teach him sorcery (魔術, Majutsu?); but Shirō proves to be talentless in almost all the fundamental sorcerous disciplines.

Kiritsugu warns his son that the life of a sorcerer is one that leads to destruction, but if he is truly set on benefiting people, he should apply his knowledge in secret and hone his craft in private. After Kiritsugu dies, Shirō becomes frustrated with his progress, feeling inadequate about his good deeds through sorcery and is unsure of how to orient his future to contribute more.

Unknown to Shirō, Fuyuki City is the setting for a secret and violent war among competing magi. For the past two centuries, seven sorcerers have gathered and engage in a Battle Royale, each gambling his or her own life to obtain the Holy Grail, a legendary chalice capable of granting wishes. The past four Holy Grail Wars have typically occurred every sixty years, with the most recent concluding a decade ago, but the fifth war has eerily started prematurely.

Each of the sorcerers, better known as Masters, is aided by one of the seven summoned spiritual familiars known as Servants, who are the reincarnations of legendary souls from all across time. These resurrected Epic Spirits (英霊, Eirei?), possess superhuman characteristics and wield powerful artifacts or abilities called Noble Phantasms (宝具, Hōgu?). A Noble Phantasm's hidden abilities may be released by invoking its true name, but casual brandishing of a Noble Phantasm is best avoided, for symbolic Noble Phantasms usually belie a Servant's identity, diminishing that Servant's competitive advantage. Specific legends may be summoned with the aid of catalysts, which are artifacts, ideas, or experiences similar or of value to the desired Servant. Only one Servant can be summoned in each war from one of seven classes: Saber, Archer, Lancer, Berserker, Rider, Assassin, and Caster.

As only astral entities (i.e. Servants) are physically capable of retrieving the Holy Grail, Master and Servant are forced to cooperate. Masters control Servants with three Command Mantra (令呪, Reiju?), which are crystallized miracles issued by the Holy Grail that manifest on a Master's body. When activated, Command Mantra permit a Servant to accomplish an incredible feat, or alternatively provide Masters with the authority to issue an irrevocable and absolute order to a Servant. When all three Command Mantras are used up, Servants are no longer obliged to serve their Masters, and as such, may freely choose to turn upon their ex-partner. In the event of a Master's demise, a Servant may choose to bind him or herself to another Master; if a Servant is slain, a Master may ally with a wayward Servant or pursue sanctuary with the Holy Grail War's impartial supervisor, who is traditionally a delegate of the Roman Catholic Church.

The Holy Grail materializes fully only when there is one Servant left standing; therefore, it is not necessary to vanquish Masters in order to win the war. However, as many Servants possess powerful Noble Phantasms and are grueling to defeat, many participants have chosen instead to eradicate Masters, who are responsible for maintaining a Servant's presence through the supplication of Mana.

After cleaning his school's kyūdō (archery) dojo late one night, Shirō stumbles upon two Servants, Archer and Lancer, battling in the school courtyard. To avoid compromising the war's secrecy, Lancer hunts down and pierces Shirō's heart with a spear. For an unknown reason, Shirō's classmate, Rin Tōsaka, uses an heirloom filled with concentrated magic, Mana (魔力, Maryoku?), to resuscitate him. Shaken and dazed, Shirō returns home only to be assaulted a second time by Lancer. Shirō weakly defends himself against Lancer, but is soon overwhelmed by the powerful Servant's attack, and is sent flying into his shed's storage room. Cornered, Shirō prepares for the worst; but before Lancer can inflict another fatal blow, a young woman outfitted in alabaster armor blocks Lancer's spear. After driving Lancer away from Shiro, she introduces herself as Saber, and greets him with the words:

“ I ask of you, are you my Master? ”

Shinn lives with his parents and his younger sister in the neutral country of Orb, but the Earth Alliance attacks Orb on June 15. Only Shinn survives when his family is caught in a crossfire between the GAT-X131 Calamity and the ZGMF-X10A Freedom mobile suits, though it is not clear whether the Calamity or the Freedom was responsible for the explosion that kills Shinn's family. Shinn blames Orb’s rulers, the Athhas, for his family’s deaths, believing that they should have surrendered to the attacking Earth Alliance Forces rather than endangering civilians in a battle that could not be won. Orb soldier Captain Todaka then takes care of Shinn and later sends him to the PLANTs, where he joins ZAFT and graduates as one of the top students in his class as a "ZAFT Red".

After graduation, Shinn is assigned to pilot ZAFT's ZGMF-X56S Impulse, and is stationed aboard the battleship Minerva under the command of Talia Gladys along with former military academy classmates Rey Za Burrel, Vino Dupre, Lunamaria Hawke, Meyrin Hawke, and Yolant Kent.

Yuki Kuran, is the adopted daughter of the headmaster of Cross Academy, and is a member of the school's disciplinary committee, which is a Guardian for Cross Academy. Ten years prior to the events of Vampire Knight, the Kuran family was attacked by Rido Kuran. Yuki's mother Juuri, wanting Yuki to live as a normal human, sealed Yuki's memories, powers and pure vampire blood at the cost of her own life, and Headmaster Kaien Cross took her in. She lost all memories of her life before the attack, but since Kaname Kuran rescued her when she was attacked by a sadistic vampire, she has been harbored admiration for him. She admired Kaname since she was small until present time. In recent chapters, upon finding out Kaname is her brother, she is shocked and it is unclear how she feels about Kaname at this point in time. Yuki is usually a cheerful and carefree girl. She has also let Zero Kiryu, a childhood friend, drink her blood, hoping to save him from insanity. She cares deeply about Zero, many times having put her life on the line to protect him, however it is unclear how she feels for him romantically. It was revealed in chapter 35 that she is the hidden daughter of the Kuran family, a family of pureblood-vampires. She and Kaname are siblings and were engaged. She does have vampire powers as well, as this was witnessed in chapter 36. As Yuki was getting over the shock of her parents deaths to save her, she accidentally made cracks in the window.

As it is shown in chapter 37, during a short talk with Zero, Yuki refers to herself as not the same as before. Zero can sense that Yuki is a pureblood and aims his "Bloody Rose" at her. Yuki claims that her vampire side "ate" her human one and the new Yuki is nothing like the one that Zero knows. Although her declaration could have been because of the pain of having Zero pull out a gun on her, especially since immediately afterwards she is creeped out by one of the popular night class boys speaking to her respectfully, saying 'it's gross' and that she expected him to keep saying 'Yuki Cross or hey you'. She may have been simply referring to the changes in her life the situation will force on her.

In Chapter 39, Yuki's best friend, Yori, finds out about her vampiric side, but still hugs her, calling her an idiot for distancing herself from her. Kaname also plans to take Yuki and leave school.

She is also sensitive to sunlight, as it was the first time she ever saw sunlight with her vampire eyes. Before her memory loss, her parents kept her confined in a well-furnished underground chamber, preventing other vampires from finding out about her. She is said to be the Kuran Princess of the pure blood royal family of Kurans. The Kurans are s

Sousuke is an approximately 17 year old sergeant within the paramilitary counter-terrorist force, Mithril. He is a member of the SRT (Special Response Team) of the Western Pacific Battle Group "Tuatha de Danaan" aboard the assault submarine of the same name under the command of Captain Teletha Tessa Testarossa. His call sign is Urzu-7 and his ID number is B-3128, and operates as team pointman as an Arm Slave specialist.

Sousuke is of Japanese descent, but has no clear nationality. His exact date of birth is also unknown. He has black hair and grey eyes, as well as a small, visible cross-shaped scar on his left chin. He is literate and fluent in both English and Japanese. He can also speak some Russian and Persian as well as several local Afghan dialects fluently. He was raised as a Muslim, but doesn't follow strict interpretations of Sharia law like the people who raised him. He is once depicted worrying more about Ramadan than Christmas in the 6th book, but his consideration is depicted on a pure combat basis ("It was a time when Soviet soldiers would lower their guard"). On a daily life basis, Sousuke is depicted as a secular character. He is shown eating pork and his refusal of alcohol is made, again, on a pure combat efficiency basis, and he clearly shows a genuine distaste for the stuff in "The Second Raid". He is capable of reciting the Qur'an from memory, probably due to his infancy in a Muslim country, but finds classical Japanese literature, poetry and history extremely difficult to comprehend.

In addition to being a capable Arm Slave pilot, Sousuke is a specialist in Arm Slave operations and maintenance, improvised explosives, small arms, survival training, anti-armor combat, trap setting and camouflage. Additionally, he is proficient in logistics, demolitions, breach and forced entry, covert intrusion, and hand to hand combat. His background and experience as a guerrilla fighter, and later a mercenary soldier has made him much more sensitive and knowledgeable about tactics and methods more commonly used by guerrillas than government trained regulars.

Sousuke is unfortunately not very good at social interaction off the battlefield. He constantly causes many problems for Kaname Chidori due to his military nature. Even in school he carries a gun with him although it is loaded with non-lethal rounds. He is also very bad at blending in with normal members of society due to his nature. That is, he has no readily available "civil" concepts about life, like entertainment or anything recreational and tends to horribly misinterpret the actions of people around him. This is shown throughout the main series when Sousuke is guarding Chidori at Jindai High, and Fumoffu! focuses mainly on this aspect. This part of his personality is indeed one of the main sources of the series' humor.

Sousuke harbors deep feelings for Kaname Chidori, however he conceals them from her due to his inability to express them. At the end of Full Metal Panic! The Second Raid, both Sousuke and Chidori have realized that they like each other, but are unable to tell each other. In the novel, A Dancing Very Merry Christmas, Sousuke realizes that he loves Chidori, but is still unable to find the courage to tell her.

Sousuke was known under various identities, such as Sousuke Seagal (temporarily), Isegar Sousuke and during his time in Afghanistan (Helmajistan in the anime), he was known as Kashim (only two characters refer to him as Kashim, one being Gauron and the other is Zaied, a former comrade from his Afghan days).

Kaname is the main female protagonist of the story, and appears to be a "normal" 16 year-old high school student at first glance. The character was taken from a friend of the authors, whose name was also Kaname Chidori, living in Japan. The discovery of her Whispered abilities attracts the attention of terrorist organizations. As a result, Sousuke has been assigned by Mithril to protect her. While Sousuke Sagara's battle intuition generally saves her from dangerous situations, she often considers Sosuke's instincts an irritant in daily high school events, leading to countless comical situations. Nonetheless, she and Sousuke continue to grow closer, to the point where they have expressed their feelings for each other.

Kaname's Whispered abilities also grant her an inherent knowledge (but not necessarily understanding) of advanced mathematics and science. It is no surprise then, that she consistently achieves top scores in these subjects at school. Her abilities as a Whispered, however, are a bit buggy. She does not know her full abilities, and also sometimes enters a near-trance, where she understands Black Technology completely.

After a point in the series, she makes it obvious to herself that she likes Sousuke, but that doesn't stop her from hitting him with her harisen. Kaname is very easy to anger, especially considering Sousuke's antics. A humorous comment made by Kurz Weber about her anger was when he saw her lose her temper and commented, "What happened to my angel?" A majority of the stunts pulled by Sousuke will cause Kaname to go into a rage fit and either hit Sousuke or chew him out. However she has a soft spot for him and when he does a good job she will often cook for him or give him a compliment.

Kaname is constantly battling with Teletha "Tessa" Testarossa for Sousuke, although the two usually end up either making fools of themselves or hurting him.

Kaname's bravery and determination came to a head in the climax of the novel Continuing on My Own. Following Sosuke's defeat by the hands of Leonard Testarossa, she gives herself up to Leonard and Amalgam to save his life. As she is picked up by the Belial's giant hand, she whispers something to Sousuke before being whisked off. After being taken by Leonard, she was imprisoned at an island villa by Amalgam. In the novel, Come Make My Day, Sousuke arrives at the island in order to save Chidori, but is unable to do so, because she's taken away in a helicopter. During the flight, Kaname is able to communicate with Sousuke, and that's when they both confess their feelings for each other, and Sousuke promises Kaname he'll find her no matter what the cost is.

She also developed feelings of guilt in the novel End of Day by Day (anime: The Second Raid) at having missed her opportunity to kiss Sousuke -- after personally giving him a haircut -- and thus having her first kiss "stolen" by Leonard Testarossa, as well as missing numerous opportunities afterwards to admit her feelings of love to Sousuke. At the end of the novel Come Make My Day she finally expresses those feelings to Sousuke while in radio contact with him and extracts an absolute promise from Sousuke that they will kiss the moment they are reunited.

In the most recent novel, Semaru Nick of Time, the origin of the Whispered is discovered to be from an accident during a Soviet experiment using an "Omni-Sphere" that occurred on December 24, 1984 -- when all the Whispered were born. Leonard Testarossa takes Kaname back to the Omni-Sphere after recovering from his wounds in Come Make My Day. There she is forced to resonate with Sophia, a key Whispered, who overtakes Kaname's personality. Under Sophia's control, Kaname is shown the illusion of shooting and killing Tessa Testarossa and Sousuke Sagara. Under Sophia's control, she leaves with Leonard for Merida Island, where Amalgam has built a machine to utilize a final ability of the Whispered; her soul crushed believing she killed her good friend and the man she loves.