Why did he take the potion?

[Commando Peach]

That's what I took away. He did it so he wouldn't be the morally confused broken man he'd become, and would only have the thought of killing Alexander and the fear of what was chasing him to spur him on. By the end you can hear it in the voice of his diaries. He's weary and afraid of himself and doesn't want to live with that anymore.