Speculations ...

Just what is going on in the manga and anime? We are led by Megumi to think that she and the Oniwabanshu are merely acquainted, but not intimately known to one another. However, the observatory/tower scene in volume 3 and in season 1 is vague and suggests otherwise.

There are some suggestions that Aoshi and Megumi are very aware of the other -- not perhaps very well-acquainted, but well-enough.

Vol 2: Manga

Beshimi (to Megumi): You escaped thinking two guards only... but by those beneath "the head" you are always under watch. be it the bedroom, the bath, ... even the toilet."

Vol 3: Manga
Kenshin to Megumi: So the Kanryu Army is made up of about 60 men . . . is that right? And the Oniwabanshu?
Megumi: Hmm... probably no more than 10. (Beshimi, Hyottoko, Hannya, Shikijo and Aoshi make 5. Okon, Omasu, Okina, Shiro and Kuro.... altogether equal ten.)

Megumi to Kenshin: ... The private army wasn't enough. Kanryu wanted Oniwabanshu so he hired a former head -- and just before (the) Meiji --the one who at the tender age of 15 became the okashira or head of Edo castle's oniwabanshu -- Shinomori Aoshi!!)

Vol 4: Manga
Kenshin to Hannya: Then answer this Hannya! The past of Megumi-dono, did you know of it?!
Hannya: How can you ask? The master spy of the Oniwabanshuu . . . knows all!

Megumi to Kenshin: Ken-san... Kanryu built a secret passage through the ceiling ... leave through that, and you can escape.
Llater...Megumi realizes Aoshi had taken that passage and escaped. Convenient that she and he both know of that passageway. Coincidence? Unlikely.

Season Two/ Kyoto Manga arc

The infamous dojo scene is rife with muddled interactions. The threat of death, which is oddly not followed except with an odd touch to the face. What exactly would have happened had not these two been interrupted?

Jinchuu arc (Manga only)

In the Jinchuu arc, Megumi and Aoshi actually work together quite a bit . . . and their relationship has progressed comfortably past the fear issue. After an awkward meeting where Aoshi comes to Megumi for an explanation of the events surrounding a mysterious occurence (which will remained unspoilt here until Viz releases the entire RK manga), Megumi actually voluntarily follows him back to the dojo, where she is later spotted having a (somewhat) heated discussion. ("idiot!"). There are curiously fun interactions between the two. It's that curious mix of annoyance and respect on both their parts which fueled some speculcation that there was something of an interest on Aoshi's side in the doctor.

...and Complications:

The two biggest complications are known as Misao Makimachi and Sanosuke Sagara.

Misao was Aoshi's ward in a sense -- and out and out worships and loves him (but in a way not explained). Her obvious care or hero-worship for him is what fuels much of the fan fervor around this pairing, despite the 9 year age difference. It is clear from the manga (and perhaps exaggerated by the anime) that Misao loves Aoshi. It is not clear whether that relationship can ever be romantic, or if it is a familial love. Misao/Aoshi fans will argue the former, while Aoshi fans scratch their heads somewhat uncertain of that aspect.. Simply put, despite the manga epilogue, what is obvious is that the two are not married five years out and that Misao is still pretty much her same old happy (and genki) self.

Megumi is Sano's elder by 2 years. Their relationship is rocky from the start to the finish; but it is evident that they too care for one another. In the anime, Sano could be said to have a crush; whether he loved her is never stated. In the manga, their interactions are not exactly romantic. Regardless, Sanosuke unfortunately runs off at the conclusion of the manga and anime. Sano/Meg fans should happily keep believing, however, there are also some major obstacles to deal with . . .

Therefore, on to the reasons . . .