Here's where you can leave me comments, critique and compliments about how I play Alyssa Hale from Clock Tower 2: The Struggle Within (Clock Tower: Ghost Head).

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What's the deal with the two journals?

It's like this - when Bates fully takes over Alyssa's body, you get ghostin_herhead. When Alyssa takes control of the body back, you get ghostin_myhead.

Additionally, Alyssa can chat with Bates in her own head when she's in control, so you may notice her doing this in logs now and then.
Bates can't chat with Alyssa however. Alyssa herself goes to sleep while Bates is in charge, a fact he may sardonically mention if you ask.

Alyssa Hale is a bit of an odd character. As such, I felt it only right to make a little info post on interacting with her.
No one is for sure exactly what Alyssa suffers from. Some, perhaps those in the asylum where she was kept after the murders, think she is a classic case of Multiple Personality Disorder (MPD), now termed Dissociative Identity Disorder (DID).
Others think Alyssa is possessed by the spirit of her dead twin, buried within the Maxwell family grave with her. This is a very likely explanation as well. Not even Bates can tell you how he came to be - he just is.

Typically, Alyssa will be in control of the body. The only time at the current moment that Bates will gain control of the body is when:
1) Alyssa does not have her amulet with her AND
2) Alyssa is in danger.

When both of these are satisfied, Bates will gain control of the body.
It is very easy to tell the difference between Alyssa and Bates. Bates is much more violent and curses quite a bit. If this weren't enough, Alyssa's voice will change from her usual medium female register to a deeper male tone.

Also, if you notice text within Alyssa's logs that (Looks like this), this is Bates talking within Alyssa's head.
Alyssa sometimes replies back verbally to him which, undoubtedly, will cause confusion. Usually though she either does not respond or responds internally.
Alyssa's own responses will (Look like this) in his logs.