In the beginning of Outlast: Whistleblower, Waylon sends the email to Miles. After debugging an Error Code 16 at the Morphogenic Engine (also seeing Eddie Gluskin being forced into the spheres and experimented on), Waylon is ambushed by Jeremy Blaire and 3 guards. Blaire orders the guards to knock Waylon unconscious with a punch, the butt of a gun and a kicks. Roughly 2 hours later, he is forced to watch the Morphogenic Engine, also being tortured by Andrew, a scientist.
An unknown amount of time later, Billy Hope takes control of the Walrider and began slaughtering the staff. In the chaos, many of the patients including Waylon escape, adding to the chaos.
Security forces were unable to quell the attacks and so the first Murkoff Tactical Division was summoned.
Waylon arrives in a kitchen, and for the first time meets Frank Manera, a cannibal. Shortly afterward, Waylon is attacked by Frank.
At this point, the first Murkoff Tactical Division has arrived.
Evading Frank, Waylon reaches the Recreation Area. Around this time, Chris Walker has ambushed and slaughtered Stephenson's Murkoff Tactical team, also impaling Stephenson on an iron pole. Miles also arrives at this time.
At the Recreation Area, Waylon meets the Twins. Eluding them, he meets a group of inmates playing basketball. He is then attacked by them after interrupting their game, but escapes. By now, Miles has met Chris Walker for the first time and has also met Father Martin.
After turning on the generator and hacking the security system, Miles is attacked by Chris Walker, but hides in a locker and escapes unharmed. Chris then makes his way to the prison.
Reaching the radio in the prison, Waylon attempts to contact the authorites, only to be stopped by Jeremy Blaire who smashes the radio beyond usage and attempts to strangle Waylon to death. Hearing Chris Walker, Blaire runs off and leaves Waylon to be killed by Walker.
Around this time, Miles is sedated by Father Martin and shown security footage of the first Murkoff Tactical team (Stephenson's was the second) getting butchered by the Walrider and is subsequently taken to a prison cell, where he is unconscious for an unknown amount of time.
Waylon manages to elude Chris and meets Father Martin, who is painting the "down the drain" message with blood. He then sees two security guards who mistake him for a Variant and block him in.
At this point, Miles has awoken and meets the Twins for the first time, who decide not to kill him because it would be "impolite" to Father Martin, who has told them not to kill Miles.
Eventually losing their patience with Miles, they begin chasing him. Around now, Waylon has arrived in the Drying Ground and has seen Eddie Gluskin behind a boarded up door, who acknowledges Waylon for a brief moment before walking out of view. At this time, Miles has witnessed a guard getting decapitated by Chris Walker and has also reached the showers, where he meets the Twins. Avoiding them, he sees the Walrider for the first time.
Around this time, Waylon miscalculates a jump and falls through a shed roof into the Vocational Block, where he meets Dennis, who tries to capture him and give him as a sacrifice to Eddie Gluskin. Miles is also harrassed by Chris Walker in the sewers. He manages to drain the the sewer and climbs down to safety. Waylon escapes from Dennis, only to end up on the third floor where Eddie resides. Shortly afterward, he finds himself hunted by Gluskin.
While initially eluding Gluskin, Waylon jumps across an elevator shaft and grabs onto a broken ladder, which collapses under his weight. Falling down the shaft, Waylon's foot goes through the elevator car and a piece of wood goes through his ankle. Waylon escapes and hides in a locker, only to be captured by Eddie Gluskin who knows where he's hiding. Eddie then sprays a gas into the locker which knocks Waylon unconscious. Twelve hours passes, during which Miles explores the asylum.
Waking up several times, he witnesses Eddie mutilating 2 patients. By the time it's Waylon's turn, Miles has already killed Trager, the insane doctor who mutilates his fingers. A heroic patient attacks Gluskin, giving Waylon a chance to escape. Eluding Eddie, Waylon jumps out a window and breaks his already-injured leg.
At this time, the second Murkoff Tactical Division has arrived to send reinforcements.
Waylon finds himself back in the Vocational Block to find a key to the Male Ward (which is where the now-dead Trager resides).
He is chased by Gluskin again after he finds the key. Unlocking the gate to the Male Ward, Eddie ambushes him and attempts to hang him.
Waylon's struggles to escape cause a sudden weight-shift, and Eddie is pulled up into the air and impaled on an iron pole, killing him.
At this point, Father Martin has crucified himself, while Miles explores the Underground Lab.
Escaping the Vocational Block, Waylon arrives at the Male Ward, where he sees three Murkoff Tactical agents examining Trager's corpse having just pulled his body out of the elevator shaft. He also sees an outside-view of Father Martin's self-immolation as a chapel is now set ablaze.
Waylon manages to elude the Tactical operatives, who have been given the all-clear to kill anything that moves.
At this point, Miles has killed Billy Hope and is shot by the Tactical operatives in the Underground Lab, but the Walrider saves him and using the Walrider, kills the Tactical agents who killed him.
The surviving agents call for backup (heard by Waylon) and the team in the Male Ward make their way there.
Waylon meets Jeremy Blaire for the last time, slumped against the exit door to the Administration Block. Hardly feeling sorry for the corrupt executive, Waylon attempts to escape, only to be stabbed in the stomach by Jeremy.
Declaring that no one can know about Murkoff's illegal experiments, Jeremy is about to deliver the final blow when suddenly he is attacked by Miles Upshur's Walrider and killed.
Waylon escapes the asylum and gets into Miles' car. Seeing a figure in the distance, he zooms in with his camcorder, which reveals that the figure is Miles Upshur - now controlling the Walrider.
Starting the car, Miles seemingly helps Waylon jumpstart the vehicle, and Waylon crashes through the gates, escaping.
We then see Waylon being told by a mysterious man named Julian, who tells him that his life is over if he uploads the footage on his camera showing Murkoff's illegal as well as immoral experiments. Initially hesitating, Waylon decides to press upload and the game ends.
Although there's probably several mistakes, this is probably the most chronologically accurate "events of Outlast & Whistleblower in chronological order" there is.