Spoilers for Disappearance lie unmarked.The Vanishing of Nagato Yuki-chan (official English title for Nagato Yuki-chan no Shoushitsu) is a Spin-Off slice-of-life manga for the Suzumiya Haruhi series. The manga is illustrated by Puyo, creator of the original Haruhi-chan manga, and details the story of a version of the Haruhi DisappearanceAlternate Universe in which Kyon wasn't transplanted from a universe run by Haruhi; instead, he's living an idle life in the Literature Club at school. Thus, everything is more "normal": Yuki is a Shrinking Violet, Kyon more of a likable Straight Man, and Ryoko your typical, responsible Class Representative.However, just because Kyon is happy in his current state doesn't mean everything is perfectly fine: among other things, Yuki has feelings for Kyon (and is completely incapable of admitting it to him), Ryoko tends to let her over-competitiveness get ahead of her, and even Haruhi herself can't stay away from the picture after she runs into Yuki one night. Soon, the Literature Club is almost where it was originally, with the members of the SOS Brigade once again populating the club, while Haruhi and her crazed search for strange phenomena are once again sparked - and there start to be hints of a Love Triangle...An anime adaptation was announced on the morning of December 18th, 2013 with the "disappearance" of the SOS Brigade website followed by a white-text-on-white-background hyperlink to the official announcement itself. Something very similar happened in 2009, which corresponded with the announcement of the Disappearance of Haruhi Suzumiya film earlier that year.
The Vanishing of Nagato Yuki-chan provides examples of:
Instead of being the listless, indifferent version of Haruhi seen initially in Disappearance, Haruhi is easily sparked back into her excitable nature (in fact she's seen already doing something mysterious in her first appearance).
It also counts as compared to the original series; despite not having the influence of Kyon in her life (credited most of the time with humanising her), Haruhi here is actually a lot less of a Jerk Ass than even late on in the series proper, being more of a slightly pushy and (of course) very independent Genki Girl and occasional Cloud Cuckoo Lander. She even has a bit of a Big Sister Mentor / Cool Big Sis dynamic going on with Yuki. This is probably due to the Lighter and Softer tone of this series in comparison with the original (which wasn't exactly Darker and Edgier itself, but nevertheless).
There are even cases when it's Haruhi playing the Straight Man to some of the idiosyncrasies of North High students, mostly Ryoko.
Tsuruya is now friends with Ryoko; and Mikuru, due to not being a time traveller with orders, is less of a complete Neutral Female and does more for herself.
Koizumi is less Ambiguously Gay (though he does retain his Yes-Man status because he's completely in love with Haruhi).
Kyon is a Nice Guy, but relatively flat and less interesting compared to the cynical and witty Deadpan Snarker in the main series, although this may just be because of the loss of the First-Person Smartass; we occasionally see his thoughts, but not the world from his perspective. He gets some of his snark and acid back when around Haruhi, so it's more like he can't bring himself to be sarcastic with Yuki.
Art Evolution: In the initial chapters, Yuki looked very little like her original counterpart and faces were often disproportionate. Furthermore, it was often nigh impossible to distinguish between Ryoko and Tsuruya, particularly in black-and-white. As of the later chapters, everything looks more natural (compare this and this).
Blind Without 'Em: Yuki is revealed to be almost entirely blind without her glasses; she's barely able to coherently go to the store and back, and she can't recognize Haruhi's face when she finally sees her without her glasses. Sorry, Kyon, but Yuki needs them.
Blunt Yes: When Haruhi and Ryoko are discussing how Ryoko's worries about Yuki and Kyon's relationship. Haruhi then follows by saying that their friendship is strong enough to handle it.
Ryoko: The more the distance between Nagato-san and Kyon-kun closes, the more it feels like they're moving further from me. And it's just... I hate it. It's lonely. I know, I know. I'm not protecting anyone. It's pure jealousy.
Haruhi:(places a hand on Ryoko's shoulder) Ryoko... (with a smile) Yeah, that's really dumb!
Bookworm: Yuki, although nowadays she's starting to put books second to her feelings for Kyon.
After the accident, the glasses-less Yuki seems to prefer books over video games
Cannot Spit It Out: Yuki for Kyon. The furthest she's been able to get is thanking Kyon for helping her do whatever-was-important-to-her-life.
Later, Kyon does spit it out but makes sure he's covered by fireworks so Yuki can't hear him, because he's confessing to having loved her alternate persona.
Charles Atlas Superpower: Tsuruya is ridiculously physically fit, mostly for Rule of Funny in an otherwise down-to-earth Alternate Universe. She declares a physically-taxing (for other people) hike to be super-easy, hints that she and her family wrestle bears on vacation, and can even bodily throw someone a surprising distance.
Chick Magnet: All of the girls appear to exhibit some degree of interest in Kyon.
Christmas Episode: The first six chapters are all about preparing for and having the club Christmas party.
Clingy Jealous Girl: A mild version. Yuki becomes distraught whenever it is hinted Kyon miiiiight be getting with another girl (it really breaks Yuki when she sees Haruhi giving what turns out to be nothing more than obligation chocolate). However, she seems to take it well when Haruhi says she "doesn't dislike" Kyon.
Club Stub: Yuki's literature club is initially about to be shut down due to a lack of members. After a talk with Ryoko, Yuki resolves to get the members needed to keep it going.
Compliment Backfire: Haruhi can't bear for Yuki to thank her for being roped into Haruhi's scheme to capture Santa.
Daydream Surprise: It initially appears that Yuki lost the card game and has to go shopping, with Kyon accompanying her. However, it turns out to be Ryoko's daydream, and in reality, Ryoko ends up losing.
Dare to Be Badass: Ryoko gives a speech like this to Yuki when she hears her club will be closed down, asking if she's willing to do what it takes to protect the club. Ryoko worries she came off too harshly, but Yuki manages to do what is necessary.
Despair Event Horizon: Yuki being told that her Literature Club is to be closed for not having enough members.
Does This Remind You of Anything??: Chapter 24 starts off with Kyon and Yuki in the forest, face close-ups showing them both blushing, sweaty, eyes closed, and breathing heavily (even the caption goes, "WHAT ARE THEY DOING?!"). On the next page, it turns out that the two are just struggling with moving through the forest late at night, trying to find a place Tsuruya mentioned.
Dragged by the Collar: Hit the club president over the head hard enough to leave a bump then drag her to the clubroom. This sort of behavior shows how much nicer Ryoko is in this series.
Dynamic Entry: Tsuruya does this once... by throwing Mikuru, breasts-first, at Kyon's head. No one was very amused apart from her. And possibly Haruhi.
Emotionless Girl: Chapter 26 has Yuki acting like this instead of her usual self. It turns out that she's trying very hard to cover up her identity amnesia (see below) but doesn't really know how to act like the original Yuki. She remains very low-key even as she grows into her "new" life but notably still falls in love with Kyon and tells him.
Likewise, everyone but Haruhi knows Koizumi is crushing on her.
Fanservice: Chapter 2 sees Kyon join the girls for supper. In the middle of conversation, though, Yuki spills all over her shirt, and briefly struggles with Ryoko pulling it off... until they realize Kyon's still there, and he just got half an eyeful.
Chapter 22 takes place at a Hot Spring. You do the math.
And the Beach Episode in chapter 36. Though oddly the full-color two-page spread of all the girls in bikinis came a couple chapters earlier when everyone was instead planning for Tanabata.
He Is Not My Boyfriend: Yuki pulls this with Kyon when Haruhi questions their relationship. Unfortunately, she takes it too far, declaring him a complete stranger (to Kyon's chagrin). Eventually she settles with "friends".
Haruhi bemoans having to constantly explain that Koizumi isn't her boyfriend, too. She genuinely doesn't feel anything other than friendship for him, though. Koizumi wishes it were different.
Heterosexual Life-Partners: Yuki and Ryoko; Ryoko is Yuki's neighbor, but visits Yuki's place so often and minds over so many aspects of her life they might as well be related.
Similarly, Tsuruya and Mikuru, who are always seen together.
Identity Amnesia: Yuki suffers from this after her accident in Chapter 25. While she still retains her memories, she no longer recognizes them as her own and is effectively a completely different person. Handled extremely seriously as the others try to grapple with what it means to treat the "new" Yuki as a distinct person, who fears being regarded as just a sickness waiting to go away when for her being "cured" sounds frighteningly like death.
Jerk with a Heart of Gold: Tsuruya. She harasses Kyon a lot for "two-timing" on Mikuru, and generally enjoys extracting whatever entertainment she can from others. Despite that, she also helps with the literature club's Christmas party, shares her family's discount at a hot springs and hotel, and hosts everyone at her family's villa and private beach during summer vacation.
Just Friends: Haruhi and Koizumi. She was the only one who gave him the time of day as a transfer student locked out of everyone else's cliques, and eventually he fell in love with her.
Last Name Basis: Fairly common; Yuki and Ryoko, despite being long-time friends, typically call each other "Asakura-san" and "Nagato-san," respectively.
Dying Declaration of Love: Yuki's alternate personality (see Identity Amnesia, above) finally manages to say it, but she knew she was reintegrating with Yuki's original identity, dying as a distinct persona.
Love Triangle: Hinted to be taking this direction; Haruhi supports Yuki's feelings for Kyon wholeheartedly, but there have been hints of her feelings for Kyon. Recently, it seemed chemistry was starting to bloom when Kyon pulls Haruhi out of the river, and she starts to feel something strange when Kyon pulls a John Smith-esque line. Then there's the Valentine's Day incident where Yuki walks in on Haruhi giving Kyon (obligation) chocolate. It's eventually clarified when Haruhi explains that she does feel a little bit of affection towards Kyon, stating that she "doesn't dislike him" to Yuki.
Even early on Yuki saw Haruhi as a rival to be emulated, even in impossible things like having a ponytail.
Later on there is effectively one involving Kyon, Yuki, and Yuki's amnesiac alternate personality. Specifically, alternate-Yuki actually confesses to Kyon just before Yuki's original identity reasserts itself, and as a result Kyon has finally wised up. Only Kyon is terribly conflicted over whether he's honestly attracted to Yuki, or if she's just a stand-in for the now-faded alternate identity that managed to steal his heart during her brief life.
Meganekko: Yuki; this is the Disappearance-verse after all.
Mistaken for Gay: When Mikuru tries to cheer Yuki on about giving chocolate to Kyon by saying that she'd be glad to get chocolate from Yuki if she were male, it comes out sounding like a Love Confession. Yuki understands the good intent regardless, but Tsuruya and Ryoko immediately tease Mikuru about it.
Mythology Gag: Haruhi attempts to recreate the "I am here" message to aliens on the field. Since Kyon doesn't know her, she doesn't run into him - and instead winds up getting Yuki to do it!
Sitting in the same exact position, Kyon responds to Haruhi's question "Do you think kappas really exist?" with a "Dunno. Maybe they do." This mirrors the Haruhi and "John Smith" conversation - it also implies that John Smith did exist at some point, meaning there could be something supernatural after all.
The John Smith scene actually happened sometime with a three years younger Kyon.
Mikuru has a star-shaped mole on her chest. Guess who knows about it? Tsuruya...wait, what?
Yuki offers Kyon the club signup sheet in the same manner she was illustrated in the light novels.
Haruhi's big reveal about her 'ambitions' is featured, but in altogether different circumstances.
Haruhi dressing up in Kyon's sports uniform so as not to stand out in North High - even down to Kyon asking her to do her hair up in a ponytail.
When Yuki gives a confusing explanation for a math problem, Ryoko says "It's like she's speaking some kind of alien language."
Some of the wishes written for Tanabata sound pretty familiar as well.
Ryouko mentions that if she explodes of tension and stress... she would get a knife and probably kill Kyon.
Just when the gang goes to a private beach, Koizumi mentions a certain prank incident that happened in Remote Island Syndrome. In fact, there are other events paralleling this story as well.
Normal Fish in a Tiny Pond: Ryoko is a good student at North High, but she's completely unable to do some of the problems Koyouen students can do.
Not a Morning Person: Ryoko regularly has to push Yuki through her morning routine to make sure the latter is ready for school on time.
Not What It Looks Like: Squared. First, Yuki walks in on Haruhi giving Kyon chocolate on Valentine's Day, throws away the chocolate she had been planning to give him, and runs out of the clubroom at full speed. Turns out Haruhi's is just obligation chocolate, identical to what she then gives Koizumi. Then it turns out that Yuki left out of consideration, and meant to present hers later - she's quite alarmed to discover she dropped hers.
Doubles as a bit of a Mythology Gag, since Kyon is infamously (and perhaps intentionally) oblivious to Haruhi's affections for him in the original (despite even having it pointed out to him on several occasions by others, notably Koizumi (which might go some way to explaining his reluctance to acknowledge it, admittedly)). It's slightly different there though since Kyon essentially wants to hate Haruhi for her behaviour towards him and others yet finds himself attracted to her anyway (or so anyone with half a brain can infer despite his unreliable narration), whereas here he clearly has no problem with Yuki, he's just terminally oblivious (possibly a case of Contractual Genre Blindness; Kyon has always been pretty Genre Savvy, after all, and now that he's the male protagonist in a romantic comedy with an incredibly shy heroine...).
There's also the theory that Kyon has retained some degree of his Genre Savvyness and what he's actually doing is waiting for Yuki to up and tell him herself. Several scenes show that he likes Yuki a lot but like Ryoko wishes she were more assertive.
Otaku: This is the artist of Haruhi-chan, after all; it's not as extreme as the other, however. Yuki does at least sneak some video games in bed.
And often winds up playing them into the morning hours, to Ryoko's displeasure.
Parental Abandonment: Ryoko's parents are working overseas, and we never hear anything about Yuki's except when a doctor mentions their absence in passing. Ryoko does almost all the shopping and cooking for Yuki, and probably a fair amount of the cleaning.
Running Gag: Yuki heeding Ryoko's advice to get an early night before important days rather than playing video games, only to not be able to sleep for excitement and stay up all night playing video games by accident. Alternate Yuki gets into the same routine with books.
Shipper on Deck: Ryoko, who ships Yuki x Kyon. In fact most of the girls do (even Haruhi, who has some degree of affection for Kyon). Tsuruya attempted to ship Mikuru x Kyon for a while, but neither Mikuru nor Kyon shared the sentiment.
There's also a few moments of Ryoko/Kyon, although it might just be that she's trying to spur Yuki into being more proactive herself.
Ship Sinking: Kyon and Mikuru however, just aren't that into each other and are Just Friends. This is in stark contrast to the regular series.
She's not molested or exposed nearly as much in this series so his knight-errant-compulsive-disorder isn't triggered. Instead Yuki shows more obvious distress and so gets more attention.
Stop Helping Me!: After the above Fanservice happens, Yuki asks Kyon what he thought of what he saw. After worrying about how to answer, he looks over at Ryoko, who holds up a cue card that says, "It was sexy (especially your belly button)."
Team Mom: Ryoko, by far. Tsuruya teases her with the idea after Ryoko maneuvers Kyon into some alone time with Yuki at the Christmas party, and Haruhi mocks her as a disapproving mother-in-law over Yuki and Kyon's relationship.
The Reveal: Haruhi's famous declaration about "time travellers, aliens and psychics", although it's in rather different circumstances to the original.
Time Skip: Third page of the manga skips forwards seven months leaving questions such as how Kyon joined the Lit. Club unanswered until later.
Took a Level in Kindness: Kyon and Haruhi are both noticeably nicer than their original characters, but the grand prize goes to Asakura.
Tsundere: Haruhi is a Type B, although it's played with a little - she doesn't get awkward when it's necessarily someone she's crushing on, just being thanked in general (she had elements of this in the original, although her Jerk Ass personality placed her more in Type A territory).
Unwanted Harem: While not all of them are into Kyon, once you get to the later chapters it's just a ton of girls congregating in the Literature Club room.
Vitriolic Best Buds: Ryoko and Haruhi. Kyon and Haruhi also. He's still a bit put off by her antics, but does seem to understand her more than almost anyone else.
Wham Line: Chapter 26. "... I thought so. Just one more thing. Who are you?"
Chapter 33: "I... Kyon, I love you." To explain, Yuki's alternate personality was prepared to "die" without telling Kyon how she felt, then spilled her guts on an impulse. Now Kyon is forced to confront his feelings for Yuki, but it screws with their whole relationship because the two personas were distinct people. Now he's faced with the loss of someone he's just realized he loves, who is still physically present but psychologically gone.