Mayor Jerry Sanders said two people on the ground were killed. Fire officials said the deaths were at a home where two children, a mother and a grandmother were believed to be inside. Officials did not immediately know who died. Shortly thereafter, the fire department confirmed that a third person on the ground had been killed, adding that a fourth person was missing and that the search had been suspended until Tuesday morning.
"We just know that four people were inside, and three of them have been accounted for," Fire Department spokesman Maurice Luque said.
The pilot, who ended up hanging by his parachute from a tree in a canyon beneath the neighborhood, was in stable condition at a naval hospital in San Diego, said Miramar spokeswoman 1st Lt. Katheryn Putnam. The pilot was returning from training on the carrier USS Abraham Lincoln off the San Diego coast when the plane went down, she said.
Putnam had no details on a possible cause. Investigators will review information from a flight data recorder, and there was no indication the pilot was using alcohol or drugs, she said.
Authorities said smoke rising from the wreckage was toxic and evacuated about 20 homes. By Monday night only six homes remained evacuated because they were uninhabitable, said San Diego police spokeswoman Monica Munoz.
There was little sign of the plane in the smoking ruins, but a piece of cockpit sat on the roof of one home, and a charred jet engine lay on a street near a parked camper. A parachute was visible in the canyon below a row of houses.
The neighborhood in the University City section of San Diego smelled of jet fuel and smoke. Ambulances, fire trucks and police cars choked the streets. A Marine Corps bomb disposal truck was there, although police assured residents there was no ordnance aboard the jet.
Neighbors described chaos after the jet tore into the houses and flames erupted.
"It was pandemonium," said Paulette Glauser, 49, who lived six houses away. "Neighbors were running down toward us in a panic, of course."
Jets frequently streak over the neighborhood, two miles from the base, but residents said the imperiled aircraft was flying extremely low.
Jordan Houston was looking out his back window three blocks from the crash when the plane passed by. A parachute ejected from the craft, followed by a loud explosion and a mushroom-shaped cloud.
Houston, 25, said a truck exploded after the driver backed over flaming debris and then jumped from the cab yelling, "I just filled up my gas tank."
The Marine Corps said the pilot was part of the Fighter Attack Training Squadron 101, based at Miramar.
The plane crashed near Interstate 805 around noon Monday about two miles from the base as it prepared to land, said Ian Gregor, a Federal Aviation Administration spokesman.
A large, busy area of the city was blocked off to traffic, creating a long backup on Interstate 805.
Students at nearby University City High School were kept locked in classrooms, but there was no damage to the campus and no one was injured, said Barbara Prince, a school secretary.
There was little sign of the plane in the smoky ruins, but a piece of cockpit sat on the roof of one home. A parachute lay in a canyon below the neighborhood.
The F-18 Hornet has long been the workhorse of the Navy and Marines since its design in the 1970's, reports CBS News correspondent Sandra Hughes. However, all F-18 models were recently grounded after cracks were found on a hinge in the aircraft. Only a small number were found to have similar cracks, and the rest returned to the air.
Steve Krasner, who lives a few blocks away in the earthquake-prone region, said he first thought the shaking generated by the crash was the long-anticipated "Big One."
He was in his kitchen when he heard two loud explosions and looked outside, then heard a larger blast.
"The house shook; the ground shook. It was like I was frozen in my place," Krasner said.
"It was bigger than any earthquake I ever felt," he said. "The flames were billowing overhead."
Ben Dishman, 55, said he heard what sounded like "a loud gunshot" followed by an explosion.
"It was quite violent," said Dishman, resting on his couch after back surgery. "I hear the jets from Miramar all the time. I often worry that one of them will hit one of these homes. It was inevitable. I feel very lucky."
The F-18 is a supersonic jet used widely in the Navy and Marine Corps and by the Navy's stunt-flying Blue Angels. An F-18 crashed at Miramar in November 2006, but the pilot ejected safely.
Miramar, well known for its role in the movie "Top Gun," is home to some 10,000 Marines. It was operated by the Navy until 1996.