After you've followed Lin up to the roof of Oasis Club and she gets the "Eureka!" Moment to use Spark to decrypt Rubilia's recordings, you can look about the makeshift hideout and find Ruby's stash of 17 Mira, which you can pilfer for "safekeeping."
After entering the Vera Tower of Fantasy for the first time to get Mi-a fixed, you can see Ruby and Mi-a fascinated with each other then later playing Rock-Paper-Scissors in the background while Lin is debriefing the player of their objectives.
In Chapter 15, quest "Unexpected Guests":
The team is walking to Tempos's control room when Brevey and Yanuo briefly break off when they see some smart servants resting at a sofa, which Brevey calls a "magic fountain". (The others—Shirli, Yun, the Wanderer, and Plotti (who is very touchy about keeping to a schedule)—stop to see what the two are doing before moving.) Brevey says that she has her own magic fountain as a special privilege, to which Yanuo replies by saying thanks to whoever keeps Brevey's room clean, implying the young scientist doesn't do cleanliness; Brevey indignantly says she was talking about her pillows.
Brevey uses her, shall we say, otaku vocabulary more often since her friend Yanuo is around to encourage it. This leads to one moment of telling the bespectacled Plotti, when they're headed into Tempos's control room, to "put on your magic lenses and find the way with magic vision~" The professional Plotti could only respond with a "Huh...?"
Character-specific
Raising KING's relationship value to the max has him sending the player some chump change (one gold) in his message.
KING's side story in Mirroria reveals that he spent all his money in Vera and has no way to pay his debts, so he asks the player to find him a job, which he all rejects due to them being menial jobs that are not his style. This paid off later in a meta sense as he became the delivery guy for a Burger King collaboration, complete with an in-game store.
One of the affinity conversations with Claudia's simulacrum starts with her noticing crowds of players crouched around beehives, AFK-farming Honey. The devs are clearly aware of what some bored players are doing!
If you talk to Samir and Huma after the main story mission, Samir will give a half-hearted apology for the pranks she's done on her side story while denying that Huma is making her do it and will give a player a gift. Opening it will show a holographic girl mooning on the player.
In Fenrir's story quest, after telling Saki Fuwa that Shelly was called away for a mission and was unable to get a limited figurine she's been waiting for months to get (which is a lie since Shelly overslept and missed buying the figurine), she's so shocked that she faints to the floor and acts like she's having a heart attack.
In Alyss's story quest, Shelly joins the player character and Alyss to collect Omnuim in the Vera Desert and luck isn't at her side during the first half of the mission as she comically drowns in a waist-high lake and gets stuck in a palm tree trying to run away from a Gooseneck Beast.
The first part of Tian Lang's trailer shows him comically bargaining with a group of sand otters, first by trying to talk to them to give him just one seed for his research, then trying to bribe them with meat, then sneaking up on them while they're distracted, causing the sand otter leader to jump on him. This ends with an Abyssant monster eating all the seeds, leading to him making a magnificent Jojo-esque face.
Miscellaneous
The CS recommendation for Ruins D-03 is 69420 — a bit too on-the-nose for mere coincidence.
In the Oasis Club, players can interact with a broken gachapon machine that develops sentience and calls itself Mr. Rio. Interacting with it daily will show it developing a one-sided rivalry with the Kun Ji noodle stand across from it, becoming somewhat of a therapist to other NPCS for mira, and later forming its cult. The player can even admit to them stealing Ruby's stash, which replies that they've had gone too far. It ends with a Hykros engineer sent to fix it promising to transfer its consciousness to a new body... but breaks its chip afterwards, to the player character's shock.
Visiting Shelly's apartment has Shelly wearing some accessories in very funny situations. She can be found either asleep while wearing a pacifier, strangling a stuffed toy between her legs while sleeping, or walking around with rabbit ears on her head.
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