My guess is events happened like this:
Red prescribes "experimental" treatment for blindness.
Everyone starts to get better.
Miraculously, other conditions or injuries on the patients begin to heal. The administrators put EVERYONE on this medication, staff included, both to further testing and to ensure that accidental injuries (which appear common) don't stop the facility's operation.
Red secretly refuses to take the medication, suspecting, for whatever reason, that something is horribly wrong. Even though it's his treatment, he sees something is just not right. Could be the voices, could be incidents of violence that occurred before Stitches's death, could be a lot of things.
Ruby kills Stitches, who gets numerous large lacerations (which later result in his distinctive stitched-up appearance). He's autopsied and put back into his cell. Red fears the worst, but covers up this death as an accident.
Ruby attacks Red. Red realizes he can no longer deny what's happening: there is something VERY WRONG with the treatment. He kills Ruby, hoping to spare her the further descent into nightmare.
Stitches comes back to life. Red realizes that nothing can stop this now, and that it's only a matter of time before Ruby comes back. He didn't save her (or anyone else) after all, and rather than live with the guilt of knowing he damned the facility or face the nightmarish realities which are sure to come, he decides to kill himself.
Red is apprehended before/during his suicide attempt and put into Cell 6 for holding. He is denied the ability to die and just escape this hell.
Most likely it was Ace who found/recovered/apprehended Red and stopped him from committing suicide, which would explain his later suicide note being direct at him.