Story explained? - SPOILERS FOR ALL CHAPTERS -

[robiwan]

Just finished the game and I gotta say that I didn't fully grasp the story. This is what I've understood so far after one playthrough:

- Emily had a difficult relationship with her parents, who did not like each other; her mom tried to divorce and take Emily with her
- Emily thinks her parents got together because they were pregnant with her
- Emily had a good relationship with her dad, who she went camping with and who taught her about astronomy
- Mom was an alcoholic and had some sort of mental condition
- Dad was a potentially violent but definitely disturbed kid, became an architect like his father
- Dad was preoccupied with death and violence from a young age and talked about a treehouse for Emily's whole life
- Emily and her mother experienced "trauma," and Emily was likely also mentally ill
- Grandfather & grandmother were very wealthy, particular, and prideful - needed everything in its place
- Grandfather's building collapsed and he eventually died (Dad did not send him to a hospital and he died in hospice)
- Mom seems to have died in the mental ward at a hospital that Grandfather designed
- Large tree growing in every part of the game, Emily does not remember consuming or wanting food or water, and she thinks everything is fake

Why were the police at Emily's house? What does the ending mean? Is Emily dead? What is the actual significance of the treehouse? Why was the whole world turning into a treehouse (with the branches growing everywhere), and what was the black sludge?

I'm sure there are metaphors somewhere in this, but it's a little too abstract for me to piece together. Anyone else get some other meaning out of this?

[Creamium]

There is definitely enough material here for someone to do a good deep dive vid on it to piece everything together.

A lot of what you listed is what I figured too, but I thought Emily's dad was also abused as a kid. It's been a while since I've played but iirc there was a separate room where he was held. The grandfather seemed like a real piece of work. Biggest mystery was actually what happened to Emily, you'd guess she was killed since she's in a limbo state between life and death, but there are no real details as to how it happened, outside of that tv screen showing that the police taped off their house. A tragedy definitely happened. I can't remember if the dad is alive or dead.

[Madam Fussy Britches]

In addition to what Creamium said, I think there was also a darker side to Emily and her dad's relationship. Yes, her mom clearly became an alcoholic and I think died in a mental hospital, where she had been sent for severe depression (based on prescription data from Acts 1 and 4), but there were also signs of her being very worried about Emily being alone with her dad (based on Emily's commentary in Act 1). I mention the nature of the mom's mental illness because the game never indicated that there was any paranoid or delusional element to it, so her concerns about Emily's well-being and objections to the dad taking Emily alone out into the secluded woods (remember, Emily only had her dad's word that her mom "didn't want to come" on these camping trips) were likely based on facts.

Long story short, I got the strong impression that Emily's dad may have been abusing her in some way and that Emily, like many children victims of abuse, was not fully aware that it was abuse. There were little hints peppered throughout Act 1, like when Emily goes into her dad's study and mentions that she loved the times where she could be around him but not actually be noticed by him. This would also gel with the "none of this is real" mentality she has throughout all of Act 1 and most of Act 2, since it sounds a lot like dissociation (a common defense mechanism for abuse or trauma victims).

I also think someone may have died in the bathroom. Remember trying to open the door with the little ducky on it (I think that must be the bathroom) and a tidal wave of black sludge came out before the door slammed shut again, and Emily thereafter refused to open that door again? Then the police cars she saw around her house (I forget what Act this is in)? This is pure speculation on my part, but I get the impression that either her dad committed suicide in the bathroom there, or else killed Emily there...

[uhsauh]

Some of my notes:
- Someone places the garbage bin in the middle of the street to cause the police car accident.
- Grand father and grand mother fight and the dad listen to the fight when he was little.
- Dad torture animals when he was young and made the animal bone into key. Adult dad had a dog and a bird, also dead.
- Dad was locked up in the basement by grandfather, confined to a chair and look at the same painting. Dad was fed frozen food all week around.
- Dad had an affair with the female architect in house 2.
- Emily doesn't like her appearance. She get scared looking at the mirror when she just wakes up. She said she has a bad relationship with the mirror in her room, similar to her grandfather looking at his biggest failure project. Emily is bullied (the dog was the only one not mean to her).
- Dad was locked up in the basement, from the basement, you can go to another floor (where the elevator can't go), and that is where dad has kept grandfather when he was ill. Grandfather's oxygen tank wasn't refilled, and he died because of it.
- In this space, upstairs in down. Basement is on the top floor in Grandfather's apartment. The psych hospital also the same. It is like the buildings in this dream-like space is all built underground.
- What happened in the hospital, such as her mom's death, is in the future. A year after Emily's death, her mom was sent to the psych hospital and died.

So the timeline is this:
- Grandfather and grandmother often fight with each other and neglect the young dad.
- Young dad tortured animal and had a lot of rage issue. As a result, grandfather locked him up in the basement.
- Grandfather was workaholic and a successful architect, who has many affairs with various women. One of his building collapsed and caused 9 death. He disappeared and hide in his own home until death.
- When grandfather got ill, dad didn't send him to hospital. Instead dad kept grandfather in the basement and leave his oxygen tank unfilled and let him die.
- Dad met mother, mother got pregnant and they got engaged. They had a daughter named Emily
- Dad had an unsuccessful career as architect. He had an affair with a female architect living nearby in house 2. Mother got mentally ill and became alcoholic.
- Mother filed for divorce. Probably dad had custody of Emily, and mother was trying to protect Emily from outside world and trying to keep her close, mother killed Emily in the bathroom
- Someone put the trash bin in the middle of the street and cause a police car accident when the police came to investigate Emily's death
- A year after Emily's death, Emily's mother died in the psych hospital, of which the grandfather designed. The hospital also looks like a church, and might have been repurposed after to be a psych hospital.

[Korikitsune]

My thought was that the dad may have killed Emily in the treehouse. Everything goes back to there, and it seems like that's where you fall into bed and embrace death; and I think it connects with the mom not wanting Emily to go camping with dad and the police at her house.

[Gwynhwyfar]

While not entirely an interpretation of the story, the following is some sort of analysis of mine...

Something I thought about was how during the five acts of the game Emily seems to go through the 5 srages of grief/death - confusion/denial, anger, bargaining, depression and lastly acceptance.

While not every act correlates to only one of the stages in that order, I found some similarites.

Stage 1: Denial
Emily is mostly confused. She finds herself in her families house, shortly after she died. Is in a limbo between life and death. She is confused because she finds out about many things that her parents never told her, like her mother being clinically depressed, her parents devorcing and her farher moving out.
Also she is, in the beginning of act 2, in denial about the police investigations. Nothing ever happens in the suburbs, so she thinks at least...

Stage 2: Anger
While Emily never expresses much anger herself, it is in the game portayed in act 3 the best, where she finds out about the anger and rage that filled her father and grandfather.

Stage 3: Bargainig
That stage is usually filled with "What if..." scenarios. The person who is grieving usually thinks about the past and what could've changed etc.
So the act taking place during the past in her grandparents appartments is fitting.
Emily tells herself multiple times that her father didn't deserve the punishments but rather should've gotten help as a child.
On a side note, I wonder why her grandmother seems so absent all the time even during this act.

Stage 4: Depression
This is portrayed through act 4, inside of the mental institution. Emily's mother was depressed afzer all and while no mental issue was ever diagnosed in the case if Emily, I am sure the girl was very depressed as well, with her parents often shouting at her ("That is the only thing they ever did together"). Also backed by the fact that she hates looking at herself in the mirror and spends most time isolated in her room, staying up far too late reading - trying to escape in another world.

Stage 5: Acceptance
This is the entirety of act 5. As she floats down the river inside the baot she lets her live flash by, she lets go of the memories until she finally finds rest in the bed inside of the treehouse.

Also, I think the treehouse was never real. It has been a symbol of hope and safety for the father during his horrible childhood. And maybe for Emily, who also had a troubled childhood, it has become that very symbol as well. That might be the reason why she finally finds rest inside of the treehouse that looks just like her own room.

Anyway, these were the thoughts I just had to get out of my system...
I hope with this I could maybe help some of you to understand the story and its stucture a little better.

Thank you to everyone who took the time to read this.

[BlackDelta]

Wow, the replies above are really helpful. The simplified Chinese version sometimes looks very weird, so it's hard for me to understand the whole plot

As for the black sludge, I guess it represents death. It seems like somebody died in the bathroom, and it is the first time we see those mud. In the process that followed, Emily kept escaping from the black mud until in the final morgue, she opened the 510 cabinet door, representing the death of her mother. At last she accepted her death and was drowned in black in her bedroom

[Scullywen]

I just finished the game and here are my two cents. Emily killed herself in the bathroom. Even though the story revolves around her family mostly, there are hints here and there that she's been going through a depression, from my point of view. All those times she says she feels "empty", those references to "pits" or "dark voids" where she would like to get lost into, her self-deprecation when looking at herself in mirrors... Also, bathrooms are places where people (sadly) commit suicide. It sounds less likely that her father killed her in the bathroom. But clearly something terrible happened in there.

The game doesn't really address Emily's depression directly, but I think this is intentional; I've read a couple of interviews with the team and they stress that being subtle with the thorny subjects in the game was key for them. I believe what we see in the mental hospital, in Act 4, is in fact the future: Emily's mother lost her mind after her daughter commited suicide. That's why the walls in her cell are covered with her drawings; they reminded her of better times, before all the chaos and sorrow. A time where her mind got stuck to.

The only weak point in my theory is the police coming at Emily's place. To be completely honest, I missed that bit, haha. I am afraid I didn't click on the TV or something. But yes, the police car is clearly a Chekhov's Gun in Act 2. So it must play a relevant role in the subtle story we don't know. Maybe Emily died somewhere else, in an accident? In the woods? Or maybe the police car was there because of the death of the kid next door, and it's a distraction for us? A Red Herring instead of a Chekhov's Gun ;).

Thank you all for putting all the pieces together above. All these theories are so interesting. And if the devs read this, congrats on a very well narrated game. Wish there would be more like this.

[Gatebase]

Here is all the title text inbetween the acts:
"Am I awake? Doesn't feel like it. But it certainly doesn't feel like being asleep."
Act 1 - The house - A moment after - Please let this be a dream.
"Only one step further, but my body feels like I've taken a thousand hour flight."
Act 2 - The suburbs - An hour after - Like a rough version of my house.
"The ground is getting hungry... I can't stay here, in case it devours me."
Act 3 - The apartments - 30 years before - The air feels heavier, as if I'm going deeper underground.
Act 4 - The hospital - One year after - My body feels tired, worn out, but I wouldn't dare to fall asleep in this place.
Act 5 - The forest - A few minutes before - I hope this river leads me to the end of this place

Some observations: This whole game revolves around a point in time. We start "moments after", then see "an hour after", etc until we end "a few minutes before". With all the time jumps it resembles someone reasoning through a chain of events and trying to find explantions. Why did the people act the way they did?
Beyond that there are some pretty mixed messages. The text would fit Emily being dead, stuck in some kind of limbo until she can make peace with what happened (not awake, not asleep, etc). But her frequently mentioning her "body" is really odd in this context. Also outright saying "please let this be a dream" right at the start makes this seem more like a traumatized girl grappling with what just happened, feeling numb and confused. It's a search, but she doesn't seem like a "lost soul" if at the start she's aware of the horrible thing that has happened (since she wishes it was a dream). Being at home "moments after", running out of the house and then stumbling through the neighbourhood "an hour after" and saying she can't "stay here" because it seems the world is collapsing on her would make some sense. But the next acts would obviously have to be in her head.

Some speculation: I think it's pretty clear that the dad is dead. We see the mom's future, but from dad only the past. For the longest time I thought dad had just committed suicide - his wife leaving him, his projects all rejected. But why would a suicide lead to such a police presence? And most tellingly - the mom feels guilty in Act 4. The wall you have to smash to get to the patient cells has "I'm sorry I was trying to protect..." written on it, while the speech bubble (somewhat confusingly) says "I'm sorry, Emily, I was trying to protect..." followed by Emily's comment "I don't want excuses, I want to get out of here". So either mom did something (like murder dad) or couldn't protect Emily from something. I'm pretty sure that rules out a plain suicide by dad. Mom might have "caused" the suicide by filing for divorce, but it would be a pretty screwed-up message to feel guilty about wanting out of an abusive marriage. The same way a plain suicide by Emily would not have been a failure of "protecting" her from something.
As someone has noted above, it's pretty heavily hinted that something horrible has happened in the bathroom at home, which would also fit the timeline. Emily found out and the game starts "a moment after" just steps away in her room. Assuming "a few minutes before" she really was in "the forest" it seems reasonable that whatever happened took place while she was out and now she just came back and found out.
I'm leaning towards a fight between the parents (there were many before) escalating because of the divorce situation and turning violent. Mom was on the cusp of leaving, there are moving boxes everywhere, she has packed Emily's belongings (that's why the boxes have her name on it). Both parents clearly have issues, but mom being under the influence a lot and deciding to move out with her daughter triggered a fight. I think she killed her husband in a confrontation that blurrs the lines between assault and self-defense. Both the moving out with Emily without asking her and the killing of dad is something she can feel guilty about and rationalize it with wanting to protect. Now there's police everywhere and Emily has to figure out what could have driven two adults who once promised to love each other to such extremes. Just my take on things.

[ZeroUnderscoreOu]

Thanks to everyone who commented in this thread and provided their point of view. It provided some insight.

I've also read theories on the Emily's dad being a murderer/serial killer (in the comments to this video), but personally I lean on someone committing a suicide in Emily's house bathroom. But it's all very vague and self-conflicting.

Personally, I'm both confused and disappointed with the story. I really dislike this "figure it on your own" thing and would really like for devs to actually comment on what the story was meant to be.

[Bliccer]

I literally don't get why ACT2 is even in there. Should it just describe the surroundings they lived in? I think the crash of the first police car you see on site is connected to the red laser pointer rather than the container/bin? Also I am not sure why the second car is burning. I think all of these situations of act2 are really just memories. The pregnant woman who apparently lost her husband and future father of her son to the accident and the fire; the rich kid who got into jail because of... spraying? ms.architect is connected to emily's dad.. the photographer? dunno
I think it is interesting though that every house is just a facade though; as if to say that all the people are just interacting on the top level and barely have anything to do with each other. But the only new information I get from that act is the affair + the "dad seemed to have a dog once" comment.
I bet there is wayyy more in there?

Also knowing about Act3, and then rereading the comment of Emily from act1 stating her parents always forbid to have a pet, felt way different than the first time around.

Where else do we see the black slime? bathroom, front door (whatever reason... just a connector?), act2: dog's hut? The sprayer's kid room (or is this literally just black paint?), there is no black slime in the baby's trolley which let me think nothing happened to the baby... on the other hand the police dude also is not covered into black slime; nor her grandfather.... so its odd this hasnt been used consistenly?

[danielendo.noemie]

I feel like the piece you might be missing is the implied sexual abuse. At least that's what I understood, and I was surprised to not see it brought it up in discussions about the game.

The father is a really bad person, potentially a psychopath as he has been killing animals since childhood.
Emily trying to empathize with him is a common behavior of childhood abuse victims. No amount of childhood trauma excuses hurting animals, and deep down she knows it. She is in denial about the things her father did.

Side note: I also suspect him of killing the neighbor's son: the outline of the child body is reminiscent of the body outline the father drew in the grandparent's home, where he hated his own father to the point of letting him die a slow, cruel death.

The mother is absent from the camping trips, but I think that the father lied about her not wanting to come - I guess he was taking Emily to the forest behind her back. In any other game a camping trip is innocent enough, but given the sinister tone of this game it would be weird for camping alone with dad to be brought up so many times if it wasn't sinister too.
Her mother probably became aware of how twisted her husband was when their dog died. Maybe she found out about the camping trips too, and that's why she wanted Emily to stay in and read instead.
We can guess the father was very manipulative and charismatic, as psychopaths often are. If the mother tried to protect Emily from him, he would have retaliated by making her into the bad guy. That would explain why she seems to like him the most.
Her mother definitely cared more than Emily knew: she tried to leave and get custody. I think her mother also called the cops on her husband, before or after Emily's death.
After Emily's death, she surrounded herself with pictures Emily drew, and she is overwhelmed with guilt about not succeeding in protecting her.

Emily mentions multiple times that she doesn't want to look at herself and that she hasn't eaten in forever - body dysmorphia and eating disorders are quite common in victims of abuse in general, and especially sexual abuse. She also mentions that her mother and her both have trauma.
Why doesn't she want to go to the bathroom? It's a place she must have dreaded in life since it's where you get naked, and it's also probably where she commited suicide since the black sludge happens in places of death.

The fact that the game ends with her getting into her bed is the most telling part to me.
The bed is out of place, placed into the treehouse instead of her bedroom.
The treehouse is all about the father: he said he would make it a place for her but it was for him, even Emily acknowledges it. He was obsessed with the idea of it.
The tree represents him. It invades the whole game, it follows Emily everywhere. It is very menacing.
And at the end of it all, surrounded by the tree, is the bed. The place where she would be most vulnerable, and where she should be safe. But despite what the note that her father left at the very beginning of the game, she wasn't safe there.

[val]

my theory is that emily was murdered by her father who then killed himself afterwards. i can see why emily committing suicide fits, and i kind of see the above argument for abuse, but i wasn't satisfied with all of the questions it left unanswered. (also sorry this is a really long notes app essay i wrote on public transportation because i couldn't get the story out of my head, so i hope it's easy to follow!).

evidence:
this isn’t going to be quite chronological with the game, but i’ll explain it in the way it makes sense to me. while emily clearly dealt with depression, likely inherited from her mother, she also notes things about her body in death and prays for it “all to be a dream” in the beginning. this seems like a weird request if she had wanted to die. there’s also no explicit indication that she wanted to end her life, no explicit relief about her death until the very last scene.

the black void in the bathroom indicates something terrible happened there, and we can interpret that it indicates something extremely traumatic, as we’ll see throughout the game. it’s not just any death, however; there are some instances of death in the game that do not have the black void present, like her grandfather's room.

in the first chapter, in her father’s study, emily mentions that she loved coming into his study before he sees her, loves to watch him work. we know her parents argue a lot and that their house is generally an unhappy one so to perceive without being perceived might have been soothing for emily, especially with her mental health struggles and body dysphoria.

as we find out in act 3, emily’s father had violent tendencies as a child that involved gory drawings and the murder of small creatures like birds. rather than seeking help for their son, his parents (also unhappy in their marriage) punished him for it. they locked him up, malnourished him, and generally neglected him. it’s likely his grandfather who orchestrated this, with his grandmother either unable or unwilling to fight against it, based on contextual clues emily notes about her grandparents and their way of living. i think the fact that they were very well off and concerned about their public appearance (indicated by their home) contributed to hiding emily’s dad’s violent behaviors.

now, back to act 2, we see an hour after emily’s death that the police have gotten into a terrible accident in her neighborhood, one that likely involved injuries or deaths of the police involved. this is also where emily explores her neighbors’ houses as well as her own.

what’s most telling however is in the yard area of act 2 — the witness report and the doghouse.

i think the witness report speaks for itself: emily’s mother, upon finding the body or bodies, calls the police for help. this, for some reason, causes the accident we see in act 2. but the timeline for act 2 is “an hour after”. that’s plenty of time for other folks in the neighborhood to call for help after the police car accident. the timeline is further confirmed by the fact that emily sees the tv in her neighbor’s house that reports the tragedy in her home — the news is reporting her and her father’s murder-suicide after it happened. so it stands to reason that there was enough time for more police / ambulances / etc to show up by the time an hour had passed.

this implies the witness report is one from the tragedy in emily’s home and the resulting police car accident. like at other times in the game, emily is not prepared to confront her death straight on yet and so conveniently cannot read it.

the doghouse also points to emily’s death at the hands of her father. like with the bathroom, the doghouse is filled with that black void, indicating not only death but a violent and personal one. as we see later, emily’s father had a habit of murdering small animals as a kid. since he was not rehabilitated or taught to manage those urges in any helpful way, those urges didn’t go away as he got older.

i think shortly after emily’s parents got married ('shortly' being relative but early enough that emily doesn’t know about the dog), emily’s dad couldn’t control his urges and murdered the family pet. maybe it was the stress of being a new father, maybe it was his continued failure at his job, maybe it was just the violence bubbling over — it could be any or all of those things. but the black void, to me, indicates that the dog’s death is a crucial piece in the factors leading up to emily’s death.

the lack of black void also indicated this to me. emily’s grandfather died sick and alone in the building he once neglected his son in. but his death didn’t have any black ooze spreading from the bed or the room he spent his final days in. we also know emily’s dad purposefully didn’t visit or help his father, nor did he allow his family to even know what became of him. although emily’s grandfather died full of regrets and without family around due to his actions, he did not die violently at someone else’s or his own hand. so no black void there, again confirming that it is reserved for particularly violent deaths or ones that are crucial to the plot.

so. my theory: emily’s father, after a lifetime of not-always-successfully repressing the violent thoughts and urges he had, has a breakdown. he’s a failed architect who cannot make his dream treehouse come to life, his family life is unhappy, and it’s about to get worse because his alcoholic, depressed wife has just sent him divorce papers. he snaps. and emily happens to be in the room when he does — maybe she snuck in at the wrong time, staying quiet and watching as she had been known to do? emily’s father becomes overcome by the strongest violent urge he’s ever had and kills emily (in the bathroom, evidenced by the news broadcast “an hour after” that shows the bathtub with a lot of blood). then, he kills himself — i’d like to think it’s out of guilt, as he did seem to care for emily a lot as shown by how invested he was in her interests (the astrology stuff, for instance) and their camping trips that emily seems to remember fondly.

emily’s mother, upon finding the bodies and carrying the unbearable burden of what has happened to her family, also snaps. but her breakdown leads to her year in the psychiatric ward shown in act 4. she keeps pictures from the before times to try to keep her spirits up but it’s ultimately not enough.

it’s possible she died of heartbreak, but i think it's clear she also committed suicide, for two reasons. first, we see many pills on the floor in room 510; emily even comments more than once on the number of pills her mom took in the hospital chapter. secondly, and more telling, is the black void once again. it shows up in room 510, transporting us back to the main level of the asylum, and acts as the climax when emily realizes her mother is in the morgue. while not violent in the same way as emily’s death or the animals’, emily’s mother’s death clearly is a crucial one to emily and is what ultimately leads emily to the final stage: acceptance of her own afterlife.

i do think the acts are meant to mirror the five stages of grief too (i think someone mentioned it in an earlier comment).

act 1 shows a lot of denial, with emily expressing incredulity at the growing trees overtaking the house and also mentioning how her parents tried to act like they weren’t unhappy with each other.

act 2 shows emily being more angry at the facade of her house not being what it should be, as well as anger at what her parents kept from her all of her life.

act 3 is bargaining. in this case, i think it’s emily understanding who her father truly was and expressing the what ifs — what if her father hadn’t been abused? what if his parents had sought to help him? what if he hadn't been the person he was? she's seeking out alternatives in order to cope with the reality.

act 4 as depression is the most apparent. emily and her mother both suffered from depression, and emily finds it difficult to reconcile with her mom’s experience in the hospital (“reduced to a bunch of notes”). it is also where emily is finally swallowed by the black void for good.

act 5 as acceptance is shown in the plot as well as the gameplay. we go from a very intricate set-up with a huge variety of puzzles to a small treehouse with only one puzzle, one we already solved in the first chapter.

the only thing that gave me some pause on my theory are the chapter titles. we assume each one is “after” or “before” emily’s death, which acts as the pinpoint around this whole game. the final act is “a few moments before [emily’s death]” which seems weird if she was murdered. but i think there are two possibilities for this. there’s the dying dream trope, which seems more likely to me. and there’s also the notion that it could be “a few moments before” something other than emily’s death. maybe acceptance of her death or eternal slumber?

anyways, this game really sunk its hooks into me — story-driven games are my favorite for this reason. if you made it this far, thanks for reading lol

[Waitsjunkie]

After looking around for explanations about the game I'm still not finding loads a few years on. There are some pretty good punts in this thread though!

- One thing I've not seen mentioned anywhere is a comment Emily makes in the treehouse toward the end. I think it's in the room with the telescope and the wood burning stove. She says that she had a lot of talks with her dad there and that he was always interested in hearing about her school friends and wanted to know their secrets. That could point toward further abuses.

- If he has been, potentially, a serial killer the map in the treehouse with pins/lines laid out in the shape of Sagittarius could be a clue to burial sites

- I'm not sure I've heard the title itself discussed much. The Almost Gone suggests Emily being dead and on the way to accepting that fact to me alongside the other clues.

[Auster]

The food and water remarks feel rather out of place throughout most of the game.

But at the end, with Emily falling asleep heavily implying her own death, the remark regarding food and water that the player can get right at the entrance of the tree house seems to tie that part up, I think.

Considering also points here in this post, it sounds like she was indeed depressed, and in the apathy that follows, she just laid down and starved to death.

And perhaps the tree house was some form of illusion her mind was creating, like schizophrenia, or a representation of the aforementioned suggestion of her making sense of all that happened and could happen, and she'd been in her bed the whole time.

[Auster]

Some further considerations:
As the game starts "moments after", maybe, indeed, she found her father dead in the bathroom, and in the shock, she laid down trying to understand what happened.

And maybe, her mother did it and Emily saw it happening, but she couldn't understand it all at first. So as she sank into bed and sorted her thoughts, she may have considered that her mother was a psychopath, which would explain the old psychopathy test in the hospital.

But given the potentially aggressive nature of her father that seems represented in the apartments, maybe she was willing to believe maybe her mother wasn't really a psycho, but rather, had just been pushed over the edge by an aggressive husband that might've also been possessive, and that didn't accept the divorce.

That would also explain, I think, how, upon entering room 208 from the hospital, Emily comments that the tree seems like either a dog happily following, or something ready to attack, which could imply she wasn't sure if her father was a caring friend, or a predator (more in the animal sense, but maybe also in the sexual sense) waiting to go for his next pray.

And with how heavily associated the tree is with his father, as well as considering as true that the dark goo is as a representation of her father's death, maybe she ultimately doesn't die, but rather, as the shock passes, and as both the darkness and tree surrounds her mind, she understands that her father is indeed dead.