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After finishing the game, I have gone on my usual trip to learn about the development and what the developer has to say. I have found the following comment by Petter Ljungqvist, developer of The Samaritan Paradox, about the ending (posted on his blog):

We don’t know exactly Jonatan’s reasons for creating the book, or the “game” it constituted, but obviously most of it was meant as some kind of ordeal for his daughter to go through, in order to achieve a potential reward. The protagonist in the fairy tale, Freja, can be thought of as a model character – just, brave, righteous, and we know for a fact that Jonatan was resentful because of Sara’s lack of interest in his work and justice questions in general.

At one point, Jonatan probably either cut the idea of implementing a reward, and instead used the book to come clean, or at least insert the confession before the reward. We don’t know if Ord stopped reading and just decided to skip the reward part, or if that was the definitive end.

We can assume that Jonatan’s resentment was partially fueled by guilt, just like his commitment in justice issues might have been a way to compensate for his horrendous deeds.

We have to regard Jonatan’s action as the result of desperation and obsession by sin and guilt, and thus not entirely logical.

We can also assume that Sara probably knew fairly well what kind of message her father had for her, which is why she was so hesitant to read it, and also didn’t question Ord’s decision to edit out the real ending (she does realize he has rewritten it – “Did you write this, Ord?”) so they both agree to move on and not talk about it. In his naivety, Ord might think he has really protected her from knowing the truth, and we don’t know if she will work with those memories, if they have been truly suppressed, or if she’s found some kind of closure.
Some interesting ideas (especially the new perspective about Sara), which I liked to read because the ending was my least favorite part of the story. And no matter what, reading about the processes behind game making or storytelling is always fascinating.