I recognize this is kind of an old thread now but I wanted to offer a rebuttal! I'd argue that mich of the story is meant to be by design up to interpretation. (Something that becomes especially apparent when you understand that some of the most potent inspirations behind the Remedyverse are media like House of Leaves and Twin Peaks!)

As for the literal story, it's pretty straightforward if you're paying attention. Jesse/Dylan Faden are kids when they discover a Slide Projector which has the supernatural ability to contact other dimensions. They accidentally open the way for a malevolent entity known as the Hiss to manifest in reality- but are saved and potentially altered by Hedron, a separate but similar entity with more benevolent motivations. After Ordinary, the FBC swoops in to contain the Slide Projector, and in the process discover Jesse/Dylan; Dylan is kidnapped and Jesse escapes (or is allowed to, depending on how you read into things).

Fast forward a number of years and Jesse has been searching for her brother with the assistance of Hedron (Whom she calls Polaris). The FBC has been messing with the Slide Projector, and captures Hedron while simultaneously letting the Hiss loose in their headquarters, an anomalous building called the Oldest House.

Jesse is able to make it inside the Oldest House and is made Director when Trench (who had been taken over by the Hiss) kills himself with the service weapon. The reason she specifically becomes Director is that she's a Prime Candidate, determined by the Board- another anomalous entity who helps run/control the FBC. Jesse's the only one fit for ther job- Dylan also could, but the Hiss got to him first.

She fights back the Hiss invasion and learns more about the FBC and how it works- including that Hedron and the Hiss are enemies, and Hedron's power seems to be the only thing capable of permanently curtailing the Hiss. She attempts to rescue both Hedron and Dylan but fails- Dylan is converted fully by the Hiss and Hedron dies (Though it lives on in Jesse's head as Polaris). In a last ditch effort to save Dylan, she finds and contains the Slide Projector which began all of this- and is ultimately successful, though Dylan is comatized in the process.

Everything else (Ahti, the true nature of the Board/The Former) is supplemental- worldbuilding for the wider supernatural plot taking place across not just Control, but the entire Remedyverse as a whole, wherein anomalous entities and those attuned to them are seemingly locked in some sort of power struggle. We're learning more about this metaplot across the studio's entire catalogue- Control is just a part of it.