Warning: All spoilers for 13 Sentinels: Aegis Rim will be left unmarked.

After the end of one world, 15 young adults are trying to make a new one. All kinds of challenges arise, some logistical, and some emotional: food needs to be grown and harvested, machines need to be fixed, and the only human beings on the planet need to learn to work together. Some already know each other. Some never had the chance to meet before. And some... well, it's complicated.

In other words: Yuki Takamiya has awkward talks about her feelings.

Apples in A Bunch is a fanfic by "TheOther1" based on 13 Sentinels: Aegis Rim. The story features Yuki Takamiya who, months into working to restart humanity alongside her fellow compatibles, still faces troubles opening up to her new companions. With some (unwanted) help from Shu Amiguchi, she works to ease tensions with their new acquaintance Tamao Kurabe, for whom Yuki has complicated feelings about after her experience with a certain robot from the simulation.

Tropes

• Actually Pretty Funny: Tamao unwittingly gets a very hard laugh out of Yuki when the former thinks that the latter is mad at Shu for rendezvousing with girls besides Yuki. Yuki can barely contain herself.
  Yuki started to say something, but only a little laugh came out. Then Yuki thought about it more. And she laughed even harder, and she fell into a squat trying to contain herself.
  "Takamiya-san?" Tamao asked with concern. "Are you alright?"
• Anchored Ship: As of the time in-universe, Yuki and Shu aren't an item - despite the apparent assumptions from everyone else. He admits to her though that he does still have feelings for her, and simply didn't want to pressure her into needing to reciprocate. The fic leaves their relationship open-ended with the implication that they will get together for real eventually like in canon. 
  "Not that my feelings have changed," he was quick to clarify, "it's just... I don't know. I didn't want you to feel any pressure. And right now, I think it’s more important that we’re friends. Do you... agree with that?"
  Yuki thought for a moment. Shu held his breath. Would she feel betrayed? Had he read the situation wrong somehow?
  "Yeah. I'd say so."
  "Great," he said, able to breathe easy again. "And hey, maybe, once things are a little more settled, we could... reevaluate. See how we feel then."
  "Maybe," she said coolly. "I’m surprised, Shu. That’s actually pretty mature of you."
• Bookends: In the first chapter, Yuki turns down Natsuno's offer to have breakfast with her, Iori and Tomi. But by the penultimate chapter, Yuki warmly welcomes the three to hang out with her, Tamao and Shu for lunch.
• Call-Back:
  • Yuki's nightmare has her confront a version of Shu wearing glasses and speaking to her in a highly-condescending tone reminiscent of Ida. Shu and Ida share DNA, after all.
  • In her nightmare, Yuki is searching for a missing Natsuno just like she had in the game. Albeit the poster she's carrying is of Natsuno as a child, which could ne a nod to Yuki being revealed to be Natsuno's biological mother.
  • Tamao is a fan of Sherlock Holmes, which was implied by 426/Aiba who enjoyed comparing herself and Yuki to Watson and Holmes.
  • Shu's messaging username is stated to have been "Tetsuya Ida" when they all started using the comms devices. And Tamao notes that what she heard about Ida wasn't pleasant.
  • Juro's "grandmother" is briefly mentioned as Shu is trying to recall whether Yuki and Tamao met in the simulation, thinking that maybe Yuki had some kind of encounter with Granny Tamao in Sector 4.
• The Cameo: Every other Compatible that's not the main trio is mostly described outside of any given scene such as Natsuno briefly speaking to Yuki from outside a room or Renya appearing only via a message thread.
• Change the Uncomfortable Subject: Throughout the picnic date they have, Yuki constantly dodges Tamao's questions regarding personal affairs like her relationship with Shu and -most vitally- her experience with 426 that's causing her to act uncomfortably around Tamao.
• Character Development:
  • After spending most of the game being generally uninterested in Shu, Yuki has since been able to become close friends with him in the few months they've spent out of the simulation, which shows that she's much warmer with him now than she had been before. It's also implied frequently that she may be genuinely interested in him romantically now, whereas before she'd rebuff any shot he had to ask her out.
  • Shu's lecherous tendencies from the game have largely mellowed out since awakening from the simulation, allowing him to better connect to Yuki on a personal level and not getting pushy with her like he used to.
  • By the end of the story, Yuki's begun to lower her walls and start opening up to Tamao who gladly accepts her as a friend.
• A Day in the Limelight: The story's POV rotates between Yuki, Shu and Tamao. All the other Compatibles mostly appear via cameos.
• The Defroster: Tamao plays this role to Yuki as the latter gradually manages to soften up to the former over the story; Tamao's general niceness and patience go a long way with Yuki's stubborn and withdrawn attitude.
• Defrosting Ice Queen: Yuki starts off still quite closed off, not unlike how she is at the start of the game, but gradually mellows out and takes to opening up to others. The fact that she and Shu are friends by the start of the story is already quite remarkable compared to how they were when they first met. And she eventually befriends Tamao by the end too after an uncomfortable first impression.
  Shu: "And believe me, I know you take a while to warm up to people. But... it’s been months since we woke up for real, you know? And I just wonder if you’ve made connections with the others. (...) And before you say it, I know you have Natsuno. And I’m really glad that I’m your friend, too.””
  Yuki: "But?"
  Shu: "But Natsuno has other friends. And so do I. And I know that back in Sector 4, you had your gang. But they’re—”
  Yuki: “Not real.”
  Shu: "Not here. Here, there’s just the fifteen of us. And I think it’s going to get pretty lonely if you only open your door for two out of fifteen."
• Don't You Dare Pity Me!: Fitting with her general fear of vulnerability, Yuki, after having just fallen off a ladder and banged herself up, lashes out at Shu for offering her help, being too embarrassed about the whole predicament. It's what sparks him to set up a blind picnic date between her and Tamao so Yuki can finally get whatever's bothering her off her chest.
• Fan Sequel: The story takes place an unspecified number of months after the Final Battle, when all the Compatibles have begun settling into RS13-Alpha.
• Fish out of Temporal Water: Because she never visited anywhere outside Sector 5, Tamao is still getting adjusted to the futuristic tech of the outside world. Even the literature from after the 1940s doesn't quite sit with her yet due to the differences in lingo and references.
  The culture shock had taken a little getting used to for many of them, but Tamao may have gotten it worst of all. During her time in the simulated earth, she had never left Sector 5, the 1940s. She never got the chance to pilot a sentinel, or even really see one up-close. The most experience she’d had with the technology of the future was when the deimos attacked Ashitaba, burning everything she’d ever known to the ground. Then later, she woke up inside an unfamiliar pod, very confused. The others had tried to fill her in, but it was information overload.
• Friendship Moment: Chapter 6 sees Yuki and Tamao finally forming a bond with each other after Yuki gets all of her baggage about Aiba off her chest.
  "Do you think we can be friends?" Tamao asked. She closed her eyes and smiled cheekily. "I promise to not be an evil robot."
  Yuki laughed.
  "Yeah, sure," she said, taking Tamao's hand and shaking it once
• Indirect Kiss: Yuki and Tamao end up sharing a cup of apple juice with each other, Yuki seemingly catching on to the implications.
  Yuki was speechless, but saw Tamao’s lips start to curl into a mischievous little grin. She’s messing with me! Yuki simply shrugged, and took a hearty swig straight from the uncapped thermos.
• Internal Reveal: Yuki discloses everything about what happened to her with 426/"Erika Aiba" to Tamao, who looks just like the robot that 426 possessed. As it's all described from Tamao's POV, it highlights just how bizarre and terrifying what Yuki experienced must have been.
• "It" Is Dehumanizing: Yuki eventually stops referring to the Tamao android with human pronouns, calling it "that thing" at one point.
• Just Friends: Yuki claims that she and Shu are just "good friends". Though the more she explains the situation to Tamao, the less certain she sounds about whether she reciprocates his feelings or not.
• Late-Arrival Spoiler: Most of the characters' interactions and motivations will only make sense to those who've played through 13 Sentinels, particularly the relationship between Yuki and Tamao/Erika Aiba.
• Mistaken for Cheating: When both girls realize that Shu planned the two to meet privately and talk, Tamao interprets Yuki's comment about Shu "doing this often" as him rendezvousing with other girls behind Yuki's back. Yuki gets a good laugh out of it.
• Mistaken for Romance: As Tamao puts it, most of the Compatibles assumed Yuki and Shu were dating due to the time they've been spending together, which Yuki clarifies is just the two simply hanging out and nothing more and that Shu isn't her boyfriend.
  Yuki: "You thought he was."
  Tamao: "Everyone thinks he is! He spends every other night in your room!"
  Yuki: "Nah, he goes back to his when it's time for bed. Must be after most people are asleep."
  Tamao thought about this for a moment, then started to giggle at her own misconception.
  Tamao: "Oh dear! I'm afraid I misjudged the situation, Takamiya-san! Oh, not that anyone was judging you! It would be perfectly fine if—"
  Yuki: "Would you stop apologizing and drink your damn juice?"
• Nightmare Sequence: The very first chapter is revealed to be Yuki having a nightmare featuring a mix of call backs to the game and her general anxieties brought to life.
• Oblivious to Love: Yuki seemingly hasn't caught onto Iori's crush on her as implied by this humorous section:
  Fuyusaka is always so awkward when I’m around. Yuki grimaced. Fuyusaka was probably scared of her. Lots of people found it hard to relax when she was around.
• OOC Is Serious Business: An offscreen example: Yuki exposits to Tamao about how Shu confessed his feelings to her before the final battle, and even asked her out amid fighting the Deimos. Though when they emerged from their pods and into the real world, Yuki was surprised to find that Shu never really followed up on his declarations to her, and over time that's both worried her and made her feel conflicted given how much time he spent in the simulation trying to be a ladies man.
  Yuki: “According to him, he used to have this fantasy of being a huge ladies’ man, so he’d act all ooey-gooey to the girls in his grade. Never got serious, though. He’s never had a girlfriend.”
  Tamao: “What about you? Does he want you to be his girlfriend?"
  Yuki: “I’m not sure. I thought, when we got out here, I’d have to beat him off with a stick. But when I got out of my pod, he wasn’t there. And then, when some of the others started to pair off, I thought, here it comes, Yuki-chan!~ I wuv you so much!”
  Tamao: “Hehe. That does sound like him! [...] He hasn’t mentioned it, has he?”
  Yuki: “Not one time. Guess it makes things easier for me. Though, he has kept following me around like a dog. Guess everyone noticed that, though.”
• Poor Communication Kills: Yuki not being able to talk to Tamao about the Erika Aiba incident just leads to Tamao worrying that she's upsetting Yuki. And Yuki just feels bad about the whole situation until she can finally muster the words to explain everything.
• Shipper on Deck: Tamao finds herself getting invested in learning about Yuki and Shu, and the hints of feelings the two might share. Eventually she starts encouraging Yuki to talk to Shu.
  "If you want to be more than his friend, or if you don't," she continued, "or even if you just want to ask him how he feels, you should speak up!" Tamao leaned in closer, and squeezed Yuki's hands. "At this moment, there are only 15 of us on this entire planet. There's no good reason there should be anything unspoken between you, as comrades, or friends, or anything more!"
• Silk Hiding Steel: The way Yuki thinks about Tamao as she gets to know her shows a clear respect for the determination beneath her gentleness.
  ''This was... not a side of Tamao she expected to see. She maintained her gentle demeanor, and yet there was something that burned brighter and hotter within her heart. An inherent flame in Tamao’s soul, that had been stoked by the circumstances of her life. Yuki could see now that this was a woman who had lived through war and tragedy, and resolved to not let it crush her. This was Tamao Kurabe.
• Threesome Subtext: While Yuki and Shu's relationship gets a lot of focus, it's also lightly implied that Tamao is slowly building something between the three of them. She and Yuki become notably close after their heart-to-heart in Chapter 6, even being comfortable being in close-quarters which is remarkable progress for someone closed off like Yuki. And the story ends off on the three of them sharing a hug.
  “If it’s an option, I certainly wouldn’t mind working with you ladies again!” He gave a playful little wink. Yuki rolled her eyes, but Tamao’s enthusiasm outshined the scoffing.
  “Of course! I’ve had a wonderful time!” She pulled Shu into a hug, which caught him off-gaurd.
  “Hey, hey! We’re all sweaty!”
  “Oh, I don’t care! Come on, Yuki-chan,” she beckoned, opening an arm for her.
  “Ugh,” she laughed, but then Tamao and Shu grabbed her arms. She was getting a hug whether she liked it or not. Luckily for all of them... she actually did like it, despite her aloof attitude.
• Trauma Button: The reason Yuki feels so uncomfortable around Tamao is because of her experience with the Tamao android possessed by 426, which the opening chapter indicates was a traumatic experience. This reaches its breaking point when Tamao unconsciously calls her "Yuki-chan" like Shu, and Yuki goes falling off a ladder while in shock.