The more I think about it....

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I would say that Agrippa's ending is generally accepted as the true ending to the game, because a) Alexander's ending makes no sense (why would Daniel choose to fail after going through the entire castle?) and b) Daniel's ending makes him a douchebag to Agrippa.

It doesn't really matter because all the endings suck. I have several different endings I wrote down that I'd like to make should I ever decide to start modding for Amnesia, which I feel would have been much stronger (some of them difficult to implement with the technology). It just blows my mind why they even considered having multiple endings. The player is not given any choice at any point in the rest of the game which is why it is artificial and feels rushed.