There is someone/something locked in the basement of Ichigaya. He is the one who sent the message to leave the apple seedling in the inn after the raid by the agents.

He is also mentioned in the Sachi ending of the VN, and probably in the sequel VNs as well.

What is his/its identity?

  • This is a fair question, but it's worth pointing out that by its nature, the answer will necessarily be a spoiler for anyone who has only read the original VN (or watched the anime).
    – Logan M
    Dec 27 '14 at 3:31
  • @LoganM I am aware of that, so whoever answers this question, please put a spoiler warning in it. But this site is spoiler-ridden to the core, if you think of it.
    – Mindwin
    Dec 27 '14 at 14:06

It is revealed in the third part Grisaia no Rakuen that:

Locked away in the basement was Yuuji's sister Kazuki Kazami, but it was her brain that was left and functioning. Ichigaya was the one who retrieved her body and built a super computer with her brain.

In the anime, the corresponding scene is at the end of episode 5, and further elaborated in episode 6 of Grisaia no Rakuen.

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