There's something very sinister about Emi. I don't just mean her tragic backstory; I mean deadly-assassin-who-knows-too-much sinister. Across multiple different routes, she's portrayed as someone very dangerous and very knowledgeable.
She's pretty familiar with Lily, Hanako, Shizune, and Hanako. There's scenes in Act 1 (such as when you meet Emi leaving the class with Lily+Hanako) where Lily clearly knows Emi and her habits and does not seem overly pleased with her presence. Emi is (was?) close enough to them to know about their tea-related activities,
which are not exactly common knowledge. What worries me even more is that she knows Misha's deepest secret,
which not even Hisao learns for quite some time in Shizune's route.
Speaking of Misha, Hisao comments that her stealth abilities are comparable to Misha's,
who was able to sneak up on Hisao to get within striking range without him even realizing in Act 1.
This brings me to my final point: Kenji. Yes, Kenji is a paranoid raving fear-monger, but even on his scale, Emi ranks as extremely dangerous.
In any route he warns Hisao about the dangers of spending time around feminist agents, but nothing matches the sheer terror
of his reaction to Emi.
Not that this is unjustified. Remember Nurse's warning to Hisao about his heart? No overexertion, and especially
do not get hit in the chest. And what does Emi do? They first meet with Emi colliding full-speed into Hisao's chest, in what could have only been a failed hit attempt.
Where does this leave us? Considering the evidence, most conclusions to be drawn are pretty scary. She's intimately familiar with the other main girls, boasts incredible stealth capabilities (not to mention her near-superhuman physical ability), nearly kills Hisao in their first encounter, and one of Kenji's most feared people.
tl;dr Emi is a powerful feminist agent who has betrayed all the other main girls (besides Rin?), possibly by going rogue. However, she still remains a highly dangerous killer that knows too much and has the strength to back it up.