Hello, this is my theory on what happened in Outlast and Outlast: Whistleblower (In chronological order)
[SPOILER ALERT]
So, Waylon sends an email to Miles. about Mount Massive Asylum, after Waylon fixes the camera in the Morphogenic Engine, he goes back into the server room where he gets forced into the Morphogenic Engine. While Waylon is in the Morphogenic Engine, Miles arrives at the asylum, gets thrown from the second floor by Chris Walker, finds the keycard for the security room, Father Martin shuts of the power.
This is when Waylon escapes the Morphogenic Engine, after Miles turns on the power and tries to open the front doors, Waylon was probably entering the Recreation Area, where he encounters the Twins, at this time Miles gets druged by Father Martin and is brought to the Prison Block. After Waylon escapes the twins, they go back to the Prison Block, where Miles wakes up, and he meets the twins for the first time. While Miles is evading the twins, Waylon finds the radio and is almost killed by Jeremy, Until they hear Chris Walker. After Waylon avoids Walker, Walker goes to the airlock which Miles opened and, attempts to smash the door, causing it to malfunction and set on fire, it explodes and causes Miles to fall to the lower floor of the Prison Block, where Miles has to escape Walker and go into the Sewers.
At this time Waylon is probably in the Drying Ground, After Waylon falls and Miles enters the Male Ward, Waylon is being chased by Gluskin, when Waylon enters the locker and is dragged to another room, where he is drugged and passes out for 12 hours. During this time Miles, kills Richard Trager, Makes it through the Courtyard, through the Female Ward, witnessess Father Martin's Death makes it to the Underground Lab. While Miles is turning off, Billy's Life Support, Waylon kills Gluskin, and while going through a hallway. see's Father Martin's death from the outside, he makes his way through and sees Trager's body, while he is going through a hallway Waylon overhears a Radio saying that there is an "Unknown Assailiant" In the basement, this is most-likely the Walrider. After Waylon Makes it out and sees Jeremy, Miles kills jeremy using the Walrider, and Waylon gets in Miles' car, and uses the camera to zoom in, where he see's Miles Walrider consumed body, leaving the asylum, Waylon leaves and uploads the footage. It is unknown what happened to Miles' after this.
Thanks for reading! Tell me if I missed anything.