Law enforcement officials never thought passengers were in danger, but they took the threat very seriously. As a result, the plane and its passengers spent hours isolated in a distant corner of the airport.
Passengers were eventually removed from the plane and forced to go through security again and a couple was taken from the plane by police in handcuffs.
Matthew Hoffman was sitting several rows in back of the couple. He and other passengers told ABC7 the couple was handcuffed and taken off by federal agents.
Hoffman says the agents came through the back doors of the plane.
"They came in rather quickly and went straight to the individual sitting in the other side of the plane and spoke to him a little bit, asked him to standup, asked him if he had any belongings with him," he said.
Alameda police say they received a call at 9:09 a.m. from a clerk at a hotel on the east end of town. The clerk said that he had gotten an anonymous call from someone threatening American Airlines Flight 24. They sent officers over to interview the clerk and they determined the threat was credible enough for them to alert the FBI.
"It was a verbal threat and that threat involved hijacking the plane," Sgt. Michael Rodriquez of the San Francisco Police Department Airport Division said.
"My desk clerk received the phone call. It lasted for about 45 seconds. The phone call went on like a rant, very jumbled, kind of made no sense. The only thing he was able to gather from it was 'American Airlines, Flight 24' and 'Hijack,'" Hampton Inn Manager Dhruv Patel said.
San Francisco police and federal agents surrounded the plane as passengers wondered why.
"The pilot came on couple times and eventually said there was a security threat and it was credible," passenger Jay Sears said.
And that was it; no other information came from the cockpit.
"It's just a weird sinking feeling of no control and not having information," passenger Randy Cohen said.
Cohen lived right across from the World Trade Center.
"I was there that day, so wow, it's like, 'this can't happen again,' so that was the feeling," he said.
Hours went by. Passengers said everyone appeared calm but these were anxious moments.
"We weren't sure there was somebody on the plane or if there was something in the plane, a bomb or something like that," passenger Glenn Dahl said.
Finally, buses took the passengers to the American Airlines terminal where they were sent through security again and their baggage re-screened. Seven hours after first leaving the gate, bound for JFK, ticket agents booked passengers onto new flights, but many had to wait at SFO overnight. Among them were those two passengers the police removed from the plane in handcuffs, not a threat after all apparently.
Passengers were tired but relieved.
"Everybody knew something was wrong but nothing was wrong and we're here safe," passenger Fabrizo Bottero said.
It turns out this was not the only American Airlines flight that was affected. When Flight 24 arrived at JFK, it was supposed to turn around and head back to SFO. That flight that would have left New York was cancelled, but American Airlines won't say how many people were inconvenienced Thursday.