Yuki Nagato (長門有希 Nagato Yuki) is the third person to join the SOS Brigade, albeit not voluntarily. She is, at first glance, an introverted, taciturn bibliophile. She later reveals herself to Kyon as an alien created by the Integrated Data Sentient Entity, and possesses supernatural powers as a result. She was sent to North High to watch over Haruhi, and over the course of her time there she comes to develop insights into being a person, as well as emotions (according to Kyon).
According to Yuki, she was created three years prior to meeting Kyon and Haruhi, with the purpose of observing humanity and its ability to evolve in intelligence, and more importantly, Haruhi Suzumiya and the data flare that she created around that time. To Yuki, Haruhi is the key to evolution. Yuki is stationed in an apartment complex where several other Humanoid Interfaces are implied to live, in room 708, alone.
Yuki remains in standby mode until "Bamboo Leaf Rhapsody", when a future version of Mikuru and Kyon come to visit her, telling her that they are from three years later and require her assistance to return to their time. After synchronizing with her future self, Yuki confirms them as acquaintances, and puts them in a room for three years, freezing time within in order to help them return. Meanwhile, another future Mikuru and Kyon come, informing her that in three years the world will be altered and that she needs to help them. Knowing that she is the one responsible for changing the world, she gives Mikuru and Kyon the tools needed to change her astray self back to normal.
Three years later, Yuki attends North High and becomes the only member of the Literary Club. This becomes a selling point for Haruhi, who immediately uses her room with only one occupant. Haruhi eventually comes to use Yuki as a part of the Brigade because of the mystérique around her.
Yuki is the first to tell Kyon about her identity as an alien; Kyon thus trusts her the most out of the three supernatural brigade members. When Ryoko Asakura tries to kill Kyon in the hopes that it would cause Haruhi to create a data explosion, Yuki saves his life, but forgets to repair her glasses, the first sign that she is fallible. Yuki is also one of the people who gives a clue to Kyon about how to get out of the closed space created by Haruhi: "sleeping beauty".
Yuki stages Emiri Kimidori in the "Mystérique Sign" incident as a pretend client in order to save a bunch of people trapped in an alternate dimension due to a logo Haruhi makes, in order to keep Haruhi entertained. She continually pulls strings from behind the scenes in a similar way Itsuki does.
During the filming for "The Adventures of Mikuru Asahina Episode 00", Haruhi accidentally causes the Mikuru Beam to become real, and thus Yuki is forced to take a large role in preventing Haruhi noticing by blocking the Mikuru Beam with her hand and injecting nanomachines into Mikuru to prevent it from materializing again.
In "The Day of Sagittarius", Yuki is revealed to have somewhat of a passion for computers and hacking, something Kyon does not fail to notice. According to the Computer Research Society's president in The Dissociation of Haruhi Suzumiya, she is very helpful and even creates a new OS that everything is compatible with.
Yuki's most prominent moment is in The Disappearance of Haruhi Suzumiya, in which due to "errors" (which Kyon classifies as "emotions") Yuki steals some of Haruhi's powers to create an alternate universe in which Haruhi, Itsuki, Yuki, and Mikuru are normal humans, Haruhi and Itsuki do not attend North High, Ryoko is a student, and there is no SOS Brigade. Kyon notices a stark difference in her actions up until that point, mainly because Yuki had been anticipating this would happen and was unable to prevent it. In the alternate world, Yuki is simply a shy, introverted girl, but clearly has true emotions because she shows fear when Kyon first bursts into her room. As she still lives alone, this becomes a problem because she rarely gets the will to eat and Ryoko must act as a concerned neighbor and bring her food. Yuki clearly takes an interest in Kyon, as she invites him to the Literature Club and tries to get him to stay for lunch by pulling on his sleeve. Kyon eventually turns the universe back to normal, after realizing that Yuki preserved his memories of the former world because she trusted his judgment and wanted him to make the choice. The Integrated Data Sentient Entity threatens to delete Yuki; however, Kyon blackmails the Entity into keeping Yuki alive.
Afterwards, Yuki places a limit on some of her abilities. In "Charmed at First Sight LOVER", one of Kyon's middle school classmates, named Nakagawa, makes a love confession to Yuki and asks her to marry him in ten years. Yuki declines, declaring that her self-control mechanism will be unable to be stable after ten years, but remains curious about Nakagawa. As it turns out, Nakagawa did not see Yuki but instead the Integrated Data Sentient Entity, and became confused by it. Yuki thus removes Nakagawa's ability to see the Entity. When Kyon asks if it was a pity that the first person to confess to her turns out to be a fake, Yuki replies that it was, "a little bit".
In "Snow Mountain Syndrome", the Sky Canopy Domain attempts to communicate with Yuki by creating an alternate dimension with a snow storm and interfering with her ability to connect to the Entity. Eventually, they cause Yuki to fall into a fever, and Yuki is forced to create a program with an ambiguous answer that eventually releases the Brigade.
Yuki plays an important part in The Scheme of Haruhi Suzumiya, besides making chocolates for Kyon and Itsuki along with the other girls. Yuki helps Kyon and Mikuru fill out their missions set by the older Mikuru, and even receives a letter herself from the older Mikuru. She reveals that she has blocked out her ability to transfer her consciousness through time, and thus believes she is more "free" in this sense (although Kyon senses she is depressed from "knowing too much"). In ""Editor in Chief★Straight Ahead!", Yuki writes a cryptic, somewhat poetic horror prose that implies confusion about her meaning in the world. In "Wandering Shadow", Yuki detects the presence of silicon data lifeforms in neighborhood dogs and manages to transplant them safely into Shamisen.
At the end of The Dissociation of Haruhi Suzumiya, Yuki claims to have caught the flu on the phone to Haruhi, which seems impossible to Kyon given that she is a Data Humanoid Interface. This is possibly due to the Sky Canopy Dominion or the aforementioned silicon lifeforms. Her current fate is unknown.
Yuki Nagato has special powers being a humanoid interface. She can manipulate the properties of environment and cast spells, what Kyon refers to as "bogus magic". She can reconstruct places and has superhuman strength, agility, and stamina, as well as the ability of rapid regeneration. In the anime, she seemingly has difficulties with distinctly human objects, such as computer mice and rifles. In The Sigh of Haruhi Suzumiya, she injects nanomachines into Mikuru to prevent her from using the Mikuru Beam. Also, as shown in Live Alive, she seems to be able to memorize the piece of music by looking at it once. In the same episode she is also able to play the guitar without any problems. As shown in Endless Eight, Yuki Nagato has the ability to remember things that are supposed to be erased by being a part of the Integrated Data Sentient Entity. Yuki also has the ability to "steal" some of Haruhi's powers and use them to her advantage, something she did in the Disappearance arc as a result of "errors". Until the Disappearance arc, Yuki has the ability to transport her consciousness through time by "synchronization"; however, she herself blocks this off after the arc in order to prevent errors (according to Yuki, this gives her more options for the future as well).
The Vanishing of Nagato Yuki-chan
Relationships with SOS Brigade members
Yuki is not shown to ever have opinions of Haruhi beyond what the Integrated Data Sentient Entity believes.
Yuki treats Kyon as a superior figure, including when he limited her power during the Day of Sagittarius incident. Yuki is very protective of Kyon, and believes him personally to be important. Yuki also trusts Kyon's judgment very much, as when she creates a new world in The Disappearance of Haruhi Suzumiya, she preserves his memories of the old world in order to give him the choice of which world to keep. Yuki may have a desire to be with Kyon, as in the Disappearance arc, even though in her perspective he is an intruder who randomly bursts into her Literature Club room saying strange things, she still invites him to the club and pulls on his sleeve to make him stay for lunch.
Because Mikuru is often intimidated by her (because Yuki often stares at Mikuru for long periods of time and also due to her powers), they aren't that close and rarely talk. The older Asahina however seems to still have such problems.
Yuki is not shown to ever have opinions of Itsuki beyond what the Integrated Data Sentient Entity believes.