>Ruby and company are blind, and are sent to a medical facility (a suspiciously Black-Mesa-esque one) for participation in experimental treatments, which may or may not have already had some sort of ulterior motive, depending on who Filbert's 'superiors' are/were.
Right so far
>One of them, Subject #6, Tom the Cat, was/became a raving berserker, and the facility had to excavate a brig for holding him securely.
From what I understand, this is incorrect. The brig is the area that was excavated, right. And it is what they find in this excavation that leads Red to discover his 'experimental' cure. This was before (and probably the reason) Tom went batshit.
>his precipitates weird experiments and so on, with Red using some of the organic material that he found while excavating the brig to treat the patients. This treatment, while curing them of blindness, also makes them susceptible to supernatural influences.
>One of them, Stitches, suffers an unfortunate accident, but nonetheless 'recovers', in the process developing mutations and possibly psychosis.
Ruby related accident.
>Red's suspicion of his own treatment is vindicated, but it already too late for him - his food has been tainted by Filbert.
>Filbert orders further experiments carried out, and all of the patients (except Maddy? Daisy) recover, but with severe mutations, 'bringing something back' with them.
Filbert was ordered to kill Maddie to see what the drug could do with staving off death. The TREATMENT is the cause of the craziness, but bringing someone back from the dead kind of 'reboots' them.
>The experience makes Ruby go crazy, and she viciously attacks Red and Tom. These attacks trigger mutations and possible insanity in both of them. The facility endures a year (or multiple-year) long cycle of horrific escapes, murders, and other calamities, held together by Filbert, Bella, and Ace.