The jet was part of VFA-125 "Rough Raiders," a squadron that trains service members on aircraft.
The Navy said they wouldn't be doing interviews at this time, but said the pilot was able to self-eject to safety.
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"It's pretty obvious to me that the pilot here was faced with something that was a catastrophic situation in terms of control of the airplane, and that's why he had to get out when he did. It's something that's a very difficult judgment call, and we've lost many pilots over the decades to people waiting too long to eject," explains ABC News Aviation Analyst John Nance.
Experts say U.S. military pilots are some of the most skilled in the world, but even in that group, incidents like this can happen.
In 2011, two Lemoore Naval officers were killed in a jet crash during a training accident not far from the base and close to where Wednesday's crash happened.
Nance is a retired Air Force pilot. He says military aviators train for a year before they get their wings, then they train an additional six to nine months on the aircraft they're assigned to fly.
"The F-35 is an extremely sophisticated airplane, and the pilots are extremely sophisticated, too. They match that with the training, either the Air Force, the Navy, the Marines, these guys and gals absolutely know what they're doing, and they know how to eject safely if something goes completely wrong," says Nance.
It's the newest fighter in the U.S. fleet, packed with stealth technology, and can fly faster than the speed of sound.
This particular version was designed for operations from aircraft carriers.
That advanced tech doesn't come cheap, as each jet carries an estimated $100 million price tag.
"A jet aircraft from scratch could easily cost over $1 billion in research and development," mentions Kevin O'Leary, who has a Ph.D. in Aviation Operations and is the President of Jet Advisors.
"So you don't want anything less than the absolute best, and that's exactly what I think we've got in the 35. It may be the last man fighter because we are going so much into automation," explains John Nance.
Experts say the investigation will be extensive and it will take at least a month, if not up to a year.
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