I really love the game. I wasn't let down by the ending because I had begun to expect that it wouldn't be a good resolved ending (because you typically do not get those lately anymore in games, due to DLC/Sequel IP planning, and in particular with Japanese games because Japan seems to really not like fully resolved endings).
But it was a wild ride. I have so many thoughts about it I hope you'll humor me a little and entertain my ramblings a bit since there's so much to digest about the game.
The Story (Ruvik)
I think it's better to think of this game as Ruvik's story than Sebastian's. Jackie Earle Haley was perfect for the role and hopefully he'll make a return. The game quickly becomes a journey through Ruvik's mind and we see that each chapter typically has some sort of symbolic value for him.
By the end of the game we know all about Ruben Victoriano. A young prodigy from an affluent family who also had mental issues, he was approached by Dr. Jimenez to help create the groundbreaking STEM system. Soon after however Ruben's life became more disjointed with the death of Laura and the severe damage to his body. His Father apparently locked him away in the basement for whatever reasons, but all that only served to drive him further into madness. In addition to Ruben becoming incensed at the Church his father belonged to for their transgressions that really bothered him.
He eventually would snap and kill his mom and dad and then set it up so it seemed like they died in an accident, thus inheriting their fortune and enabling him to continue the work on Stem without any issues. However, he later realized that Jimenez was taking all the credit and accolades for the work (and likely began to realize the organization he worked for was corrupt and perhaps involved with the Church as well). Becoming distrustful of the man and learning more about the organization he worked for, he began to take measures to try and fend them off while trying to complete the work on his own. It seemed hinted that Valentino became a serial killer dumping bodies after he finished performing his experiments on them. His mansion would also burn down due to unexplained reasons.
He underestimated Jimenez and the organization though, and they eventually caught up to him and captured his work, using himself as the catalyst and first test subject for the STEM. Subjecting him to the same experiments he had done to others, his body was eventually completely destroyed with only his Brain remaining connected to the STEM. Though apparently there was no way to make the system work without Ruvik connected to it, and attempts to use other subjects to make it work ended up with those subjects brain dead. At some point they found a subject which did work, Leslie Withers. I imagine they probably thought about using him as a replacement for Ruvik, however they inadvertently gave him exactly what he was looking for, a replacement for his body. Thus setting up the premise for the game.
Somehow Ruvik manages to manifest himself in the real world and enact a massacre at the Beacon Hospital, this drawing the attention of our protagonist Sebastian and his partners. All of them are somehow knocked unconscious and connected to the STEM system (though it seems Julie was able to withstand the effects and connected herself willingly in order to move forward with her own mission). Ruvik uses the STEM to create a world of his own image filled with his inner demons and memories to torment and ensnare his victims. It is unclear just how many victims total he integrated into his machine. We can only assume that all those "MISSING" posters we find in the "Hub" world are his victims. I would imagine most of the characters encountered in the STEM world are possibly leftover fragments of those tormented souls, like Valerio.
In the end Ruvik manages to get to Leslie and seemingly absorbs him. Though Sebastian imagined himself defeating Ruvik's machine-self and squashing his brain, we see in the ending that the brain jar was already empty (though that begs the question what happened to his brain? I assume the organization probably took it to study) and Leslie walking away without anyone other than Seb noticing.
Sebastian
Where people would likely be disappointed with the Story is in terms of the other characters and their own arcs. Particularly Sebastian who has his own personal story told from within the Hub world and is left unresolved. We know that Sebastian was married to another Cop named Myra and they had a daughter Lilly. One day however Lilly and her babysitter were killed in what was thought to be an accident. However Myra began to suspect it was foul play and began her own investigation, becoming distant to Seb in the process, which to outsiders made it look like she was becoming unhappy in the marriage. She eventually disappears without a trace, which to outsiders looks like she willfully left Seb due to his drinking problems, though Seb later finds evidence that she was investigating the organization behind STEM and got too close. He resolves to find out what happened, though we are left to assume this occurred just before the incident at Beacon Hospital.
What is not touched upon much in the game is that Seb seems to show many times that he finds his surroundings familiar in addition to Ruvik implying that he knows of Seb. I suppose it is possible that Seb would have visited the Victoriano manor in the past given how much police activity likely took place there, but one would think he'd have remembered those incidents with more clarity.
Seb's biggest plothole is the existence of the "Hub" world and what it represents. In it we have the mysterious Tatiana the nurse as well as a "cell neighbor" whom is left purposefully unobviously unidentified (though many believe it is the missing journalist who was investigating the organization and Ruvik's role in it). The world itself seems to change a few times. One time in between chapters it turns black and white and nurse Tatiana is covered in blood, and following her leads him to the Church Chapter. Another time Ruvik presumably uses his influence to change it up to resemble the Manor, and later to symbolize the decaying world crumbling around them. Nurse Tatiana disappears once Seb realizes she went "Missing" in the real world. It is worth noting he typically returns to this world once uncovering memories of his life with Myra.
Seb's visions are harder to categorize given how quickly they flash before him. We see one where he's presumably being strapped down and being led by gurney somewhere (possibly being taken to STEM). In another weird one we see him from his point of view in a STEM terminal being shot at by what appears to be himself. I suppose it is possible that being connected to STEM, he maybe was receiving visions from the others who were connected and looking at things from their points of view.
In the end I suppose many of these plot points may end up going nowhere, but it is fun to think about.
The Chapters
I wonder what everyone's thoughts are regarding the Chapters themselves and the settings and symbolism behind them are. I did enjoy that most chapters seemed to be creations based on Ruvik's mind, while others seemed to represent the obstacles that were put in place to prevent Seb and co from reaching the metaphorical core of the world.
Chapter 1: I felt as an intro it was ok, but I think I would have preferred a more gradual descent into darkness than the dive that was taken. It made it more obvious that the world was fake and that what was happening was most certainly not real.
Chapter 2-3: I suppose the reason for this location to exist was because it was near the hospice that Leslie was often kept at, and was likely created from Jimenez' memories and used by Ruvik to draw Leslie out.
Chapter 4-5: As Ruvik pinpoints Leslie's location, I think a battle of wills takes place with Ruvik creating a recreation of the Hospital in his own twisted mind and thus we are left wandering the halls of a place where Ruvik's inner demons, such as Laura, are given form.
Chapter 6: I found this Chapter very interesting in the way it was presented, using the photographs in the Hub to give it an eerie progression. But it is clearly created from Ruvik's distaste of the church (complimented by the articles and recordings found during this chapter).
Chapter 7: The Keeper is pretty straightforward which combines the Church catacombs with an industrial workshop fitting for the entity which symbolizes the hatred and secrets that are kept locked within Ruvik's mind.
Chapter 8: This is the Chapter I just do not get. There is little contained within in terms of documentation and no cutscenes to add any points. I suppose the only thing it could symbolize is Seb trying to ascend from the depths he was taken down to in his search.
Chapter 9-10: Going directly to the heart of the matter by peering into Ruvik's past and uncovering the sordid details of his upbringing and work. First with a visit to his Manor to uncover what caused his trauma and what dark secrets he was working on for STEM, and then to his "workshop" to see just what Horrors he brought upon those who were unlucky to be chosen for experimentation.
Chapter 11-15: At this point the game changes to the now obvious goal of getting to the Hospital where it all started to stop Ruvik. While no doubt trying to lure Leslie to him, he also throws everything he can at Seb and co to stop them from interfering.
Man there's so much to digest with this game. I'm definitely looking forward to seeing the holes filled in hopefully in new installments and expansions.