After the four women had understood the little girl that had spontaneously appeared in the Scarlet Devil Mansion's ground was actually Meiling's precious camellia given life, the natural progression of their investigation was to figure out how this strange event had happened.
Pathouli had apparently put enough magical wards on that flower to ensure that, despite the ambient magic and faith in Gensokyo, it would be completely unaffected. The flower would remain just a flower until the end of time. This clearly was something that did not happen, as evidenced by the young girl that was now in their company.
Well, natural progression for everyone but Meiling that is.
Sentence doesn't quite make sense, especially due to it's placement. You probably should move it up a paragraph and possibly expand upon it. It's quite vague.
Thankfully, it seemed that Patchouli had heard them. A shower of elemental magic shot up from a space between several bookshelves, a clear sign where the magician was. The party quickly descended to where the source of the signal was and was greeted to the sight of Patchouli Knowledge at a desk, books and notes sewn about haphazardly as she attempted to puzzle though whatever conundrum was plaguing her.
"were greeted with the sight"
Pathouli knowledge regarded the sight with a single, unimpressed cough, "I fail to see what is so fascinating about a newborn youkai."
"Knowledge"
"And one of the most expensive and precious objects in the entire mansion," Remilia added, folding her arms dourly, "So Patchouli. Given [that] you gave me your personal guarantee that the flower wouldn't ever gain sentience, pray tell… how did this happen?"
Realising that there would be no talking her way out of this, Patchouli relented. Pushing herself away from her research and notes, albeit it seemed with great reluctance, the magician looked into Remi's eyes and nodded.
While this was going on, Reimu and the others watched Patchouli conduct her inspection with looks ranging from keen interest to bored impatience, however none of them dared to approach the two for fear of interrupting the magician while she worked.
"to bored impatience; however, none of them"
Reimu was of the 'bored impatience' variety. She honestly didn't see what Remilia found so fascinating about this whole process. As far as Reimu was concerned, as long as she got her answers and knew this mess wasn't going to start a chaotic mess that would blow up in her face, she would be satisfied.
Perhaps change 'mess' in "event"? You use 'chaotic mess' later in the sentence.
Alas, Pathouli was taking a long time to finish her inspection. It had been almost an hour since the battery of tests, ranging from magical scans to a physical inspection, had started.
"Patchouli"
"I will have to do more research, but preliminary findings suggest she's some kind of a dryad." Patchouli informed them curtly, "Which is curious because…"
God good, she only knew of one other flower youkai in Gensokyo…
"Good god,"
"I'll need to run more tests before I can give you more concrete results. However, now that I've determined exactly what she is, where to proceed from here is fairly straightforward," Patchouli informed them, "I will be able to narrow down the exact reason of the change, but will require some time to do so. In the meantime, please leave me alone. Distractions would only slow me down."
"will"
Remilia nodded, clearly familiar with Patchouli's methods. "Fair enough. Sakuya, please return to your normal duties. Also please find one of the fairy maids…"
"…she really is my little flower, isn't she?" Everyone turned to look at Meiling. Still sitting in the same chair she had been for the past hour, the Chinese youkai was staring at Cha Hua with eyes that seemed to be on the verge of tears and a very conflicted expression.
More a personal preference, but I find a dash '-' better indicates interruptions than ellipses '...'
Missing comma.
"Request granted." Remilia replied with undisguised concern, "I had actually been about to order Sakuya to find one of the fairy maids to take over your duties for the day. This... this is something you need to have time to think about Meiling. I mean, considering your history…"
"I was actually about to"
"Mei-mama!" The little youkai rushed over to hug her mother excitedly, only for find the taller woman [to] gently rest her hands on her shoulder and push her away. "M-Mei-mama?"
Not sure if the 'taller' is needed. So far Cha Hua's been described more as a girl than a woman, so just "tall woman" ought to suffice.
"S-Sorry, Cha Hua." Meiling said laboriously, clearly struggling to retain her composure, "I… I need you to stay with Doctor Patchouli, okay? She… she has some tests she needs to run on your to make sure you're healthy, alright? Ma… I want you do help Doctor Patchouli, alright?"
"you"
"…I'll come back later, Cha Hua." Meiling nodded hesitantly, pusing her 'daughter' over to Patchouli, then quickly turned to Remilia, "By your leave, Mistress."
"pushing"
"turning"
"..What the hell was that?" Reimu muttered darkly to Remilia, wondering what the hell was going through Meiling's head at that moment that she'd leave her emotionally vulnerable and confused daughter alone like she just did, "That's her daughter. How could she-?"
Sentence is a bit fragmented. Perhaps "wondering what was going through Meiling's head that would cause her to leave her emotionally vulnerable and confused daughter alone like she just did"
Still not quite happy with it...can anyone else chip in?
With Meiling having vanished off to parts unknown and Patchouli busying herself with research, Reimu saw little point in lingering. As she had no idea where to even begin with talking to Meiling and she has zero research whatsoever, Reimu decided the most productive thing she could do given the circumstances, was to head back upstairs and get changed into something more dignified than the pink polka-dot pyjamas she was wearing.
"had zero interest in research"
Missing comma.
Indeed, she hadn't been the only one who had taken her leave. While Remilia had decided to remain in the library, obstinately to conduct her own research into 'a personal problem', Sakuya had disappeared via the magic of time stop shortly after declaring she needed to get back to her chores. With both of the other investigators pretty much calling off the hunt for now, Reimu followed suit.
"shortly afterwards, declaring she needed to get back to her chores."
Taking to the air with [the] full intent on getting her morning routine sorted out before the day got any crazier, Reimu had been halfway to the exit when she saw a panicked Koakuma making a beeline towards her. "Oh, what now?"
"of"
"Reimu! Reimu, I need your help!" Koa pleaded as she flew up to Reimu, completely flustered, "Ms. Usami's gone missing again and I can't find her! Help!"
"her"
Oh, now this was a problem. [The?] Scarlet Devil Mansion was not the kind of place that anyone should be allowed to run around [in] unsupervised at all. While it was perfectly safe for Reimu because of her reputation and power, Renko had no such protection. Any number of horrible things could befall an unwary guest, and soon Reimu's mind was awash with the many possibilities of what could happen to her charge.
Missing comma.
Still not happy with the second sentence, the one about the Scarlet Devil Mansion...feel free to chip in, people.
"Wait, you've lost her three times just this one night? Didn't she [go] back upstairs to sleep?" Reimu said as she and Koakuma flew together, watching the rows of bookshelves below them in hopes of locating the wayward tourist. "Didn't she get tired at all?"
"over the course of"
"asked"
"peering in-between "
Well, that explained why Reimu didn't see Renko anywhere this morning. Oh, she should have seen this coming a mile away. Trust Yukari to have a friend who is about as energetic as she is sleepy!
"hadn't seen"
"was about as energetic as she was lethargic!"
Reimu pointed at the sight with one hand, wondering if her eyes were deceiving her. Koakuma turned to see what had caught Reimu's attention, and found herself likewise stunned by what she was seeing. The pair was so astonished, they stopped in mid-air, just hovering there as they tried to absorb what they were seeing.
"were"
Missing comma
Walking across one of the Voile's many bridges while reading an open book was Renko Usami, their missing tourist. Behind Renko was a small procession of five fairy maids, following after the woman like a row of ducklings waddling after their mother. The arms of each fairy maid was occupied with holding a tall stack of books that was about as tall as they were, resulting in quite a strange sight.
"procession of five fairy maids" or "small procession of fairy maids"
"were"
One human woman, who wasn't [even] looking where she was going because her face was in a book, was leading around a bunch of fairy maids who were carrying stuff for her.
"due to her face being buried in a book,"
"How's that happen?" Reimu said to herself.
"How did this"
"asked"