After I read "Ulysses" several years ago, I had no clue what it was about, despite having completed the novel. I'm in the same boat with Remedy's "Control", having just finished it. Here is my guess, based on the game's dozens of text artifacts, audio logs, and videos. I'm also toying with the notion that maybe the whole game is taking place during a therapy session-- but I'll go with this for now:
Brother and sister have alcoholic and potentially abusive parents, who humiliated the sister by showing embarrassing pictures to people via a slide projector in the home. The kids steal the parent's projector, and take it to the garbage dump to throw it away. An oft-bullied friend from school tags along, together with some other children: seven in all.
Some kind of industrial accident happens at the dump, the children are all injured and wind up in the hospital, in critical condition. The surgeon in the hospital is a fellow named "Dr. Casper". Out of the seven hurt children, there are two prime candidates for survival: the brother and the sister.
The sister recovers, but the brother dies after a brief period in a coma, much to the extreme chagrin of a disheveled Dr. Casper: "he showed so much promise!" Time passes, and as the sister grows into adulthood, she is totally unable to cope with her guilt at having brought her brother, and others, into danger at the dump-- and in fact, as a coping mechanism she maintains that her brother is still alive.
She develops an escapist fantasy world, constructed from Jung's "collective unconscious" elements including popular culture artifacts such as melodramatic detective novels and science fiction films. She tries to take a clerical, secretarial job to support herself, but the daily grind makes her miserable and she quits, incorporating her office experience into her fantasy-- where she's in control, and the boss.
In this fantasy world of hers, paranormal elements caused the accident-- like a glorified ghost story-- while the police and first responders were actually government agents sent to cover things up. Her brother didn't die: he was "abducted". This is a classic coping mechanism, where her subconscious can remove her culpability over what happened.
Her psychiatric condition eventually becomes so severe that she gets committed into a mental institution, and undergoes in-patient therapy sessions.
The therapist tries to get her to admit that the incident was actually an industrial accident, and not some kind of government conspiracy-- and also that the girl's parent's alcoholism was partly responsible for the sister's present-day mental health issues. The sister insists: "No! It was not an industrial accident! My brother is still alive too, and I'm going to go see him!"
Putting that plan into action, she escapes from the psychiatric ward to "see her brother", and works her way Eastward. This is where the game begins. Over the course of the game, she is told by numerous "characters" in her fantasy universe that her brother is actually dead-- but she violently lashes out in denial each time.
Her delusions are so great that like "Flat Earthers", she has to make up totally implausible explanations to cover the gaps in her worldview: for instance, how a building so large it can hold an entire rock quarry inside of it can exist in the middle of New York City without anyone noticing ("it has this veil, where people can't see it!"), and even amusingly exclaims at one point, "they even transported the entire town dump into the building!"
At one point, as she reflects back on her life she visits a room with "photographs" from her past, for example picking books up off the floor in high school. "A-hah!", she says, "All of those years I was insecure, the government really was tracking me! See, I'm not crazy!"
Deep down, even she realizes that she's become like one of the kook "conspiracy theorists" who call into the "America Overnight" radio show. But then, finally and over the course of the game, she ends up back to her home town, and in fact to the very dump where the accident had occurred.
It's only by revisiting this "ground zero" scene that she can finally accept that her brother is dead, as she destroys the "Hedron" in her fantasy. Only after this happens is she able to take control of her life, along with the responsibilities of a well-functioning adult: she becomes "the director".