After not hearing from the suspect, identified as 38-year-old Marin County resident Peter James Thomas, police drilled several holes into the hotel room at the Extended Stay Deluxe and inserted a camera into the room. They were then able to confirm that the suspect had died and they entered the room.
The woman who was in the room with the suspect, believed to be the man's girlfriend, is being interviewed by police but she is not believed to be considered a suspect in the standoff or Sunday's attempted grocery store robbery.
Thomas had outstanding warrants in Marin County fior burglary, weapons and drug charges.
Eighty police officers are both outside and inside the hotel and have been since around 10:30 a.m. Wednesday. Police say a man, whose name has not been released to the public, fired a shot from his second-floor hotel window when police came to arrest him.
"It was fired in the direction of 580; we can't confirm exactly where it landed," said Chris Rardin with the California Highway Patrol.
Concerns that the next shot might hit someone in a vehicle on the freeway caused the CHP to close a three-mile stretch of I-580 at one point, causing a massive traffic backup.
Thursday morning, the gunman's view of the outside world was blocked by an eight-by-ten sheet of metal steel suspended from a crane. The one-inch thick piece of steel offers bullet-proof protection from the public.
The steel went up just after midnight, at which time the freeway was reopened.
"An officer came up with the idea of hanging a steel plate," said Marge Rohrbacher with the San Rafael Police Department, adding that a company was quick to come out to the hotel with a crane and the sheet of steel.
Police have been looking for the suspect since Sunday when he allegedly stabbed a San Rafael grocery store worker after being caught shoplifting. Police say he then drove away in a stolen car.
Police found him at the Extended Stay America hotel Wednesday morning. Law enforcement defended their decision to shut down the highway after the gunman shot in the direction of the freeway.
"Our ultimate goal is always to resolve this peacefully and not have any injuries at all, and that's ultimately what we want," Rohrbacher said. "We will take the time we need to accomplish that."
Several law enforcement agencies from nearby communities, including San Francisco, have joined with San Rafael negotiators. Additionally, a SWAT team from the FBI is also on-scene.