The pilot, who is from the 144th Fighter Wing out of Fresno, is alive and okay.
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Officials say the pilot is a highly experienced F-16 pilot instructor with over 2,000 hours of air time.
It's unclear exactly what this fighter jet was carrying but it was some sort of ammunition.
Officials say out of precaution several streets were blocked off on Friday as they work to recover the plane.
The closure impacted a nearby cemetery, causing ceremonies to be canceled.
The fighter jet belonged to the South Dakota Air National Guard in Sioux Falls.
Officials say the pilot was trying to land at March Air Force Base in Riverside County after a routine training mission.
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But something went wrong.
The pilot was able to eject, parachuting down, and officials say he is doing good.
The aircraft did not explode but the crash ruptured the sprinkler system.
Employees at the warehouse were able to escape without any serious injuries. They were treated and decontaminated after being exposed to debris.
The fire chief says officers who went in to clear the warehouse after the crash were exposed to something but could not say what and taken to the hospital for evaluation.
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First responders evacuated surrounding businesses, blocked off streets and now the work to clean up the wreckage begins.
It's unclear what type of ammunition the fighter jet was carrying.
But we do know the threat to the public is minimal, even though they have a wide perimeter set up.
The warehouse the plane crashed into is a distribution center for Chik Fil-A.
In a statement, a spokesperson said due to the crash they have not been able to provide daily delivery and many of their locations are out of a couple of products.