long thread is long.
Anyways, my theory.
Shortly before PoFV has begun, Eirin has read about Reimu's past deeds, and learned about a research project led by Yumemi, in the incident that became known as Phantasmagoria of Dim. Dream. Eirin then thought that the flower incident that would happen every 60 years would be her chance to perform a similar research, yet remain unsuspected. So, she has poisoned certain subjects with a synthetized substance, in order to gather data of these subjects' biological processes while they're under battle. If Eirin was successful, she would be able to improve her battle-enhancement elixir, and also gain more understanding of the subjects' behavior under stress and pressure, and how their thought processes translate into their magical abilities.
So, after the test subjects have been given special discounts on Eirin's medicines and have consumed them, the test subjects are then exposed to Eirin's pheromones, after the medicine has taken effect. Special care was needed, in order to ensure each subject would behave as planned, due to the fact that the medicine for humans are different than those made for youkai. But the effect was the same: The subjects felt an irresistible urge to serve Eirin and please her, even though Eirin herself wasn't in their minds at the time. As the flower incident was happening, the characters were being defeated, one by one, but the power of the medicine kept them fighting each other, so that when their spiritual strenght waned, they would draw it from the incoming fairies, who exploded with such force, that their nearby colleagues would also die with an equally strong explosion, which also blew away most of the onscreen projectiles. The heroines' desire for victory wasn't only directed to defeating their colleagues, it would also make them draw more spiritual power from the corpses of the fairies and the defeated magical avatars (a.k.a boss summons) of their colleagues. The barrages often became too dense for them to dodge through, so they would scream in silent desperation for Eirin while releasing part of their acquired magical power, in order to keep struggling towards their goal.
Finally, when Reimu became victorious, Eirin greeted her in a cold night; Reimu's muscles were still trembling, tensely, and her mind was in a cloud of confusion for what she has done to her friends, and fairies, and also for the mental ordeal of having to outsmart her defeated opponents, who couldn't stand the overpowering barrages of quickly expanding bullet rings, the increasing amount of orbs that appeared at random places, and the homing bullet rings that took out so much screen space from them.
Reimu was extremely tired, but her willpower allowed her to raise a hand towards Eirin. And, after being pleased by the success of her experiment, Reimu was taken to Eirin's private basement, chained, undressed and raped, by Eirin, who then instilled Reimu with nutrients, for the purpose of nourishing her, so that she could be subjected to Eirin's embryo-fetal growth medicine. After Reimu gave birth to her and Eirin's child, still weak and unable to process much of what was happening to her, Eirin proceeded to inject yet another substance into the child, which overloaded its neural system instantly, killing it.
Feeling that Reimu was getting weaker, and the effect of her drug would wear off soon, Eirin felt satisfied, further motivated to do more similar experiments, and decided to get rid of the baby corpse, by making Reimu eat it.
So, the incident has ended, though Reimu didn't remember much details about it. It looked like a normal incident, to her, and she thought that she was too tired after "solving" it, that she fell asleep. However, occasionally, she would remember about her opponents looking bigger than they really were, and instinctively, as if it were a self-defense mechanism, she would become afraid of trying to relive that experience, a thought that created an unrest, a tension between her mind, and her will.
tl;dr: this is what can come out if we ignore the gameplay-oriented answers :V (shall I stop now, or do you want more of this?

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