Seattle-Tacoma International Airport officials grounded flights temporarily during the drama but later said normal operations had resumed.
Earlier, the Alaska Airlines reported "unauthorized take-off' of the plane at Seattle-Tacoma International Airport in Washington".
In a video statement, Constance von Muehlen, Horizon Air's chief operating officer, said that the plane departed around 8 p.m. and that no other passengers or crew were aboard.
Two F-15 fighters were scrambled from the Portland airport and followed the plane as it flew over the region, the FAA reported.
"This is not a terrorist incident", Ed Troyer with the Pierce County Sheriff's office wrote on Twitter.
The plane crashed into Ketron Island, it said.
The Q400 is a 76-seater turboprop aircraft.
An air traffic controller called the man "Rich", and tried to convince the man to land the airplane.
The Pierce County Sheriff's Department has a number of vessels on scene, while the U.S. Coast Guard is on scene as well.
Annual Perseid Meteor Shower Coming This Weekend
We can always hope that, after scattered afternoon showers and storms, the clouds will dissipate and give way to a starlit sky. College football begins in less than four weeks for UVA, with the Hokies playing their first home game on Sep. 8.
Witnesses heard several planes flying low over the South Sound Friday night.
Alaska Air CEO Brad Tilden said the company was still "gathering facts" to understand why and how the mechanic was able to steal the plane.
The unidentified 29-year-old ground service agent was pronounced dead after the crash, Pierce County Sheriff Paul Pastor said.
Then the passenger plane pilot "did a complete loop ..."
"The FBI continues to work with our state, local, and federal partners to gather a complete picture of what transpired with tonight's unauthorized Horizon aircraft takeoff and crash", the agency said.
"I just want to keep talking to you and if you keep going to the Olympic mountains we can't hear you", the controller says.
Jenkins described the island as remote, dark and sparsely populated.
Morse added that her mother, who lived closer to the crash site, texted about eight minutes later to say that her whole house shook.
This is a developing story, more information to come.