The Disappearance of Nagato Yuki-chan ended early in the summer, appropriately in an awkward spot between seasons. I was left with a bit of an odd sensation of insecurity–exactly whose disappearance did the title refer to, the familiar and beloved Nagato presented back in 2006, or the 2015 Yuki-chan full of open human emotions? Both are certainly applicable with their own definitions and circumstances. Both evoke a sadness that never fully vanishes at the series’ end.
It is immediately clear to fans of the KyoAni series that Satelight’s story takes place in a completely different reality. Gone are the supernatural entities of gods, ESPers, aliens, and time travelers. We are greeted by the sight of Yuki-chan absorbed in her handheld instead of quietly reading a novel. Her glasses have been updated from prop status to a necessity. She is painfully shy, particularly in Kyon’s presence, and openly wears her emotions for others to see. All physical similarities aside, this Yuki-chan is another person entirely deserving of her own show. Though I was surprised at meeting someone other than expected, I slowly warmed to this girl with an obvious crush, love for Christmas turkey, and addiction to video games.
Then came the shift, where my gradual appreciation for the new Yuki-chan was blocked by a return of someone familiar and dear. Thanks to a near-death collision, the present Yuki’s personality buried itself deep within, leaving behind a Nagato devoid of any sense of emotional connection to her memories. I would not go so far as to say that this Nagato is a match to the one of old—she’s still a normal girl without any of her alien data manipulation—but the similarities are uncanny. She shirks the handheld in favor for novels, approaches math with the standard practice (none of those pink clouds and kyun-kyun couplings!), and eliminates superfluous communication with others. Other than Ryoko, the only person in whom she exhibits any interest is Kyon. This interest begins as a curiosity in the memories colored with affection that Yuki-chan carries, and then grows into Nagato’s own desires to remain together with him.
When this series was announced, I was very curious as to the meaning of “disappearance” in the title. Perhaps it would mirror the film, The Disappearance of Suzumiya Haruhi, and remove Nagato Yuki from Kyon’s reality. That obviously did not turn out to be the case, as she opened the series. Then I thought the word pointed to the disappearance of alien Nagato Yuki. That belief held out the longest and was almost undeniable to me until the accident more than halfway through the season. Their stances swapped places; now the one seemingly vanished was the softer Yuki-chan. Watching the newer Nagato examine her memories and move through the motions of her life, I realized the multi-functionality of the term. The closer Nagato’s feelings for Kyon matched those of Yuki-chan’s, the further away my expectations for her character stepped. Like Ryoko and Kyon, I love all versions of Nagato Yuki as their own persons. Disappearance became rediscovery.
Anime B&B 
I really enjoyed this series. As someone who thinks that the real title of the earlier Disappearance movie should be “The Rejection of Yuki Nagato”, since I found that to be the most significant part of the film, it felt to me like the universe set up in this show was the same as in that movie, but without Kyon rejecting Yuki (and thus everyone else becomes a normal person). I really enjoyed the budding romance between the two of them, helped along by the alternately motherly and wingman Ryouko. But I was a bit annoyed with Kyon’s inability to pick up the concept that Yuki-chan would like him as much as Nagato-san did.
Considering the ‘disappearance’ tag, I think it could mean any, or all of those things. Here’s another possibility: The Yuki-chan that we are introduced to and get used to through the first part of the show does, in many respects, disappear forever after the personality shift to Nagato-san. After she knows that her alter-self confessed to Kyon, she becomes much more comfortable with the idea of being with Kyon. Perhaps it’s knowing that he won’t outright reject her or that she can muster the courage to confess again, but she is definitely changed after that, not shying away from him, not overreacting at all to his touch or his closeness. Instead, she revels in it even as Kyon agonizes over it. I really liked the person that Yuki became, and was disappointed by the end of the show with what felt like a cop-out not-really confession by Kyon. It’s not as if the show will continue any time in the future. Let them be together.
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I really, really like your additional proposal for “disappearance” as applied to Yuki-chan, before the character transition. Right before her return in that dream state as she talks to the alien-esque Nagato-san, she’s told of the confession. She’s also informed that she’ll forget everything the moment she wakes up. But that isn’t how it seems afterward, is it? Gone is the stumbling dialogue and uncontrollable blushing. When holding hands longer than expected, it’s Kyon who overreacts and pulls away. As much as I like the matured Yuki-chan, I miss her vulnerability; perhaps Kyon feels the same way, as if this Yuki-chan is yet another new person he must get to know.
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I feel like separating the ‘vulnerability’ from the ‘awkwardness and uncertainty’ is a good thing. To me, the lasting effect of Nagato-san’s confession isn’t the confession itself, it’s that Kyon doesn’t run away. And it feels like that’s the thing that maybe emboldens Yuki-chan to to not be so scared around him, to not be as afraid of and overly conscious of any intimacy that happens. I like that because that behavior gets tiresome to me.
As for Kyon, I don’t know if thinking about Yuki even came into it in the last arc. It was mostly just thinking about how he felt about her.
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