The family of John Patrick Bedell, 36, also spoke out, saying they were devastated by the news of their son's action and pleading for privacy.
"We are devastated as a family by the news from yesterday," they said in a statement. "To the outside world, this tragedy is the first and only thing they will ever know of Patrick. To us, he was a beloved son, brother, grandson, nephew, and cousin. We may never know why he made this terrible decision. One thing is certain, though -- his actions were caused by an illness and not a defective character."
San Benito County, Calif., Supervisor Reb Monaco, who represents the family and has known them for 35 years, said he would have never suspected that Bedell could be so violent, although he acknowledged the shooter was mentally unstable.
"He didn't have any mental problems growing up," Monaco said. "He went to school with my children, he was very intelligent. I never associated him with any mental issues until maybe the last 10 to 12 years. Recently, he was not functioning mentally."
"I don't want to blame it on a marijuana addiction -- it certainly, I don't think helped it. He became very troubled," he added.
Bedell's parents reported him missing last month. According to the missing person report, they had not heard from or seen their son since Dec. 30, 2009. The shooter's father, Oscar, stated in the report that his son, John, had been in an argument with his brother three weeks before that date and was staying at an unknown location in San Jose, Calif.
On Jan. 3, Bedell's mother, Karen, got a call from a highway patrol officer in northern Texas who pulled Bedell over for speeding, according to the missing person report. The officer asked her if she thought Bedell was a danger to himself or others, and she advised the officer that he was OK.
Bedell returned home on Jan. 11, when his mother called the sheriff, saying her son was impaired and agitated after she confronted him about a $600 purchase from a shooting range in Sacramento. But by the time police arrived, Bedell was gone.
On Jan. 18, he returned home one last time and told his parents not to ask any questions about where he has been.
In February, he was pulled over in Reno, Nev., and charged with driving under the influence and possession of marijuana. He posted bail and continued on his way to Washington, D.C.
Per the missing person report, Bedell's father was worried about his son's safety and stated that he had a medical marijuana card, and that he had been detained before for medical evaluation. Oscar Bedell also said his son did not have any family or friends on the East Coast, where he told the officer in Texas he was heading.
Bedell had been an electrical engineering graduate student at San Jose State University but missed enrollment for 2010.
"He was not in school at this time," Monaco added. "He had one more class and he didn't return to school for some reason -- he went on a road trip of some kind."
Monaco, who last saw him nearly two years ago, said Bedell has two younger brothers and lived with his parents most of his life. He didn't know if the man had any friends.
Bedell drove to Washington, D.C., from California in the past few weeks, Pentagon Police Chief Richard S. Keevill said today, to conduct what was essentially a suicide mission.
At 6:40 p.m. Thursday, he approached one of the entrances to the Pentagon and began firing after officers asked him for an access pass. The California native was well-dressed, in slacks, a white collared shirt and blazer when he opened fire, police said.
He had two semiautomatic weapons concealed in his clothing and a large amount of ammunition. Police said that he may have uttered something before opening fire, but what he said was unclear.
"The officers were emphatic about saying he was very calm, that there was no distress," Keevill said. "He had his arms down at his pocket. We see folks come up to the Pentagon every day that have their passes in different places. He reached into his pocket. They assumed he was going to get his pass out. He came out with a gun and just started shooting."
Bedell was shot twice in the head and died at 10 p.m. Thursday night at the George Washington University Hospital, the FBI said today. The two officers he shot, Jeffery Amos and Marvin Carraway, were released. There was also a third officer involved, the FBI said, but his name was not released.
"Those injuries were grazing injuries," Keevill said. "The police officers were able to return fire."
Gunman Had Troubled Past
Bedell had brushes with the law in the past and his Internet musings mentioned charges for marijuana possession as a reference to the government's intervention in his life.
Last month, Bedell was pulled over in Washoe County, Nev., for failing to signal at the light when police found 76 grams of marijuana in his possession. Bedell was charged Feb. 2 with driving under the influence, unlawful possession of drug paraphernalia and possession of marijuana. He was supposed to appear in court March 2.
This was not Bedell's first run-in with the law. He was arrested for cultivating marijuana and for resisting a police officer in California in June 2006.
Monaco said Bedell's parents tried to intervene multiple times and get him help, but he wouldn't listen.
As for the motive behind Thursday's shooting, police say they are not certain yet but they are investigating Internet postings in which Bedell wrote and recorded audio expressing his anger toward the government.
"The moral values of individuals and communities are increasingly attacked by a political system where deceit is routine and accepted and the only standard is power," he said in one online video.
One Internet posting with the name JPatrickBedell on it talked about suspicions that the attacks of Sept. 11, 2001, were staged, calling them "the September 11 demolitions."
The suicide mission seemed to be another attack aimed at the government, but those who knew Bedell expressed surprise.
"He used to talk to me when he was younger about politics," Monaco said. "He was always interested in political issues, issues related to the economy and relaxing marijuana laws. But I certainly never associated him with any conspiracy theories.
"This is going to sound bizarre, but he was a very, very gentle young man, I mean, I never associated him with any violence on any level," Monaco said. "He was a very gentle, quite intellectual young man."
The Keevill said that the gunman appeared to have acted alone.
There was "no indication at this point [of] any domestic or international terrorism at all," he said.
Police also confirmed today that a second individual taken into custody was only briefly detained and was released after authorities determined that he had nothing to do with the incident.
This is not the first case of a fatal Pentagon shooting. In the late 1980s, a person with mental issues came to the Pentagon and shot a Naval officer, but "that was many years ago, before 9/11," Keevill said.
Sources say authorities will look at whether the federal government and the military are increasingly becoming a target.
Just a few weeks ago, Joe Stack flew his plane into the IRS office in Austin, Texas, after leaving a lengthy manifesto in which he told the IRS to "take my pound of flesh and sleep well."
In November, Army Maj. Nidal Hasan went on a shooting rampage in Fort Hood, Texas, after railing on the Internet about the United States' foreign policies and wars in Iraq and Afghanistan.
ABC News' Mary-Rose Abraham, Luis Martinez, Richard Coolidge, Sarah Netter and Ned Potter contributed to this story.