The threat prompted the evacuation of about 3,200 students and 180 staff members, along with an hours-long search for explosives.
The incident began about 8:45 a.m. when authorities at Camp Pendleton said 22-year-old Daniel Morgan was missing and a search of his barrack turned up a note that suggested he had, or was going to, place explosives at the school.
Camp Pendleton officials immediately notified the Orange County Sheriff's Department, prompting the evacuation on the first day of school.
Evacuees were initially taken to the school football field after authorities deemed it safe. But because of hot weather conditions, authorities moved everyone into the gym.
Anxious parents gathered outside the campus, making calls and texting their loved ones inside.
"He said, 'I'm fine, I'm fine. We're in the gym," said parent Aimee East. "He seems OK."
Three students were examined for mild heat exhaustion. They were released to their parents and were going to be OK.
"We had some students complaining of the heat, so that did have a big role in making the decision to release the students," said Marc Stone of the Orange County Fire Authority.
Students were released just before 1 p.m. with freshmen being let go first. Students without cars were directed to a nearby Albertsons parking lot.
Deputies conducted a room-by-room search of the campus, but no explosives were found on campus. Orange County Sheriff's Department spokesman Jim Amormino said Morgan turned himself in at a hospital at Camp Pendleton.
The motive for the threat has not been determined. Morgan was being interviewed by military police.