I finished the game for a third time tonight to get the platinum, and each time I gain more and more appreciation for it. After my first playthrough, I had no idea what happened at the end of the game but I've picked up on a number of things and have a few interpretations.
1. The entire game consists of the dying thoughts of Anne's father. The big thing here is that the very first shot of the game is from the perspective of her father (it is clearly *his* hands), but the rest of the game is from Anne's perspective. Even when you are seeing things from the perspective of other characters towards the end (the priest, the mayor, Cord, etc.), you still see them from the perspective of Anne -- it's her hands that you see, not their's. The very first scene is the only time when the game is not clearly seen from Anne's perspective, perhaps because this is the only scene that takes place in reality.
What is even more striking from the first scene is that you see her father locking up a blue box, but when you unlock the box towards the end of the game, it's a red box. Like the red door and the red bird. I really feel like this is significant. I think her father is reflecting on his life, how he may have risen through the ranks of the FBI or whatever by means of betrayal. He may have actually, in fact, been the person who investigated Judith Ortega.
Everything that is red represents his daughter going in a different path from him. The red envelope is her escape from the prison cell, rather than ratting out Maria. The red bird and the red door are seen at times, opposing the bison. I believe the bison is the representation of Anne's father in his dream.
You hear the machines at the hospital bed at times during the game (the tape recorder at the beginning after Anne receives her FBI badge; when Anne is holding the captain's hat in Halperin's office), not because they are Anne's memories, but because her father is dying as we experience this game from his point of view.
At the very end of the game, Anne "kills" the bison as the red bird emerges from her broken mask, after the sequence when she opens the box. And in the very last scene, when leaving town, the "unsolved case" is solved. The missing boy is walking out of town wearing, you guessed it -- red. Anne's father has regrets about his own life, and is overcome with the fear of her following in his footsteps. As he dies, he is able to let go once he has acceptance that she will chart her own path in life, and not make the same mistakes he did.
2. Anne is an unreliable narrator, but it is her experience that we play. I think it's just as likely that everything above is represented symbolically into Anne's experience, which actually does take place. Anne experiences severe anxiety and stress after being presented with the assignment of investigating Maria. Her dreams and hallucinations are a representation of that as the story plays out. In this interpretation, I still hold on to the idea that the bison is her father's influence (the shape of the broken half key that Anne holds onto also kinda looks like a bison's head -- the full key is blue in the opening scene, but the half key is a dull brown). And everything red represents the path that her father didn't go in.
So then, what actually does happen? At one point, I wondered if Anne died when falling off the tree branch. Everything after that point became weirder and seemed like wish-fulfillment. For example, Maria's necklace just sitting on the rocks like that felt very fishy.
Here's what I think happens: After the "acid trip", after you walk into the light of the UFO, you're back in the field where you found the necklace. Only now, those rocks aren't there. And you see the boy running off into the woods. I think this is when Anne wakes up from the fall -- everything that happens in between was a dream. She goes down there to find the necklace (and does), but also spots the missing boy, who runs off. She patches things up with Maria, they go out searching for the boy and find him walking along the side of the highway with his guitar.
So those are my two interpretations. I'm still leaning a bit towards the first one; I really think that first scene of the game is a big hint towards what follows. But it could also very well be a combination of the two.
One thing that I noticed, but I'm not sure what it means. You see a dark shadowy figure in the doorway after the scene where the boy catches his father in the act. It looks like the shadowy figure is that of a girl. I'm pretty sure that this is the same figure that steps out of the UFO and takes the boy away. What that all means, I don't know.
I think it's a pretty brilliant, well-thought out game. I really got a lot out of it by replaying it a few times.