The Pentagon is facing urgent questions over how it lost an $80million aircraft that was finally found crashed in a field just 80 miles from its base following a frantic 28-hour search.

The Marine pilot of the F-35B Lightning II took off on Sunday from Joint Base Charleston, South Carolina – but an unexplained issue forced him to eject.

The plane was flying in tandem with another jet, which returned to base after the mishap rather than following the pilot-less aircraft.

The second F-35 pilot, who had also been on the training mission, landed without any problems, base spokesman Tech. Sgt. James Cason said.

The stealth jet’s transponder, which usually helps locate the aircraft, was not working ‘for some reason that we haven’t yet determined,’ said Jeremy Huggins, another spokesman at Joint Base Charleston.

It forced the base to issue a humiliating appeal for assistance in finding the jet – even launching a hotline for tips, which was mercilessly mocked online. ‘So that’s why we put out the public request for help,’ said Huggins.

Scorched earth from the crashed fighter jet is seen on Monday in South Carolina

The F-35 went down only around 80 miles from its base, north of Charleston, South Carolina

The jet appeared to crash through trees before catching fire in the field

He said the aircraft’s sophistication made it even more complicated to find.

‘The aircraft is stealth, so it has different coatings and different designs that make it more difficult than a normal aircraft to detect,’ Huggins said.

Meanwhile, it emerged on Monday night the Pentagon in 2019 was concerned the plane could be vulnerable to attack by hackers – which may have sparked panic during the 28-hour search mission.

Marine Corps Commandant Eric Smith issued a two-day stand-down for all aviation units both inside and outside of the United States, which was set to take place at some point this week.

No units will be allowed to fly until they have a two-day discussion about safety measures and procedures, according to an email seen by ABC News.

The plane was finally found on Monday afternoon in a county only 85 miles north of the base, with wreckage of the plane located in a well-tended field.

Aerial footage showed debris in a copse beside the field, where trees had been knocked over. The field had a large area of blackened scorched earth.

It is not known whether locals informed the military of the crash, which did not appear to have happened in a remote region.

A neatly-kept farm appeared to be the focus of Monday’s search

The plane crashed in a field only 80 miles from the air base

A helicopter is pictured during the search on Monday for the wreckage

Search and rescue teams are pictured on Monday amid the hunt for the plane

Nancy Mace, a South Carolina representative, said on Monday she had been briefed on the search, but described the incident as extremely embarrassing.

She said there were urgent questions which needed answering as to how one of the world’s most sophisticated fighter jets could vanish.

‘And guess what: They didn’t have any answers,’ she told local news station WMBF.

‘They don’t know if the plane is in the air or under the water. They could not tell me the precise location of where the pilot ejected or where the pilot landed.

‘And we’re talking about an $80 million jet. How does it just disappear? And how does the Pentagon ask for the public’s help in finding it?

‘It’s just a huge embarrassment.’ Several hours later, it was confirmed the plane had been found – but questions remained.

‘Personnel from Joint Base Charleston and @MCASBeaufortSC, in close coordination with local authorities, have located a debris field in Williamsburg County,’ the base wrote on X.

‘The debris was discovered two hours northeast of JB Charleston.

‘Members of the community should avoid the area as the recovery team secures the debris field. We are transferring incident command to the USMC this evening, as they begin the recovery process.’

It now emerges that US defense officials raised concerns about safety issues concerning the F-35 as far back as 2019.

A report from the US government’s General Accountability Office (GAO) four years ago warned the $80 million aircraft’s system ‘provided a back door for hackers.’

The jet operates on Lockheed-Martin’s Autonomic Logistics Information System (ALIS), which watchdogs said can be infiltrated by malware that spoofs the system to stealthily feed false information, taking perfectly serviceable aircraft out of service.

Meanwhile, a report by a Government watchdog warned that the F-35’s weapons systems could be overtaken by ‘relatively simple tools and techniques.’

Lockheed Martin was tight-lipped on Monday about the crash, but said in a statement: ‘We are aware of the mishap involving an F-35B from Marine Corps Air Station Beaufort and are thankful the pilot ejected safely. We are supporting the government’s investigation.’

The military has not shared details about the cause of the incident, but the 2019 report sheds light on the flaws plaguing the Department of Defenses’ most expensive weapon system.

POGO, a watchdog, released a report in 2019 showing that nearly every software-enabled weapon system tested between 2012 and 2017 can be hacked – including the F-35.

The agency wrote: ‘Despite years of patches and upgrades, the F-35’s most combat-crucial computer systems continue to malfunction, including the Autonomic Logistics Information System (ALIS) maintenance and parts ordering network; and the data links that display, combine, and exchange target and threat information among fighters and intelligence sources.’

‘As in previous years, cybersecurity testing shows that many previously confirmed F-35 vulnerabilities have not been fixed, meaning that enemy hackers could potentially shut down the ALIS network, steal secret data from the network and onboard computers, and perhaps prevent the F-35 from flying or from accomplishing its missions.’

Military officials appealed in online posts Sunday for any help from the public in locating the aircraft

A Director, Operational Test and Evaluation report from 2017 showed a 26 percent fully mission capable rate across the entire F-35 fleet.

POGO’s Dan Grazier shared: ‘The fully integrated nature of all F-35 systems makes cybersecurity more essential than for any other aircraft.’

In the report, he noted that the jet has low ‘fully mission capable’ rates, which means it is ‘rarely ready for combat.’

The Marine Corps Air Station at Beaufort – where the pilot took off from on Sunday – is about 35 miles south west of Charleston.

It is home to several units of 2nd Marine Aircraft Wing, including the Marine Fighter Attack Training Squadron 501 which flies F-35B Lightning IIs. 

About 4,700 military personnel serve at the 6,900 acre site which uses a large air-to-air combat area off the coast of South Carolina and Georgia, along with an air-to-ground combat and bombing range in Georgia’s McIntosh County.

It was home to a heavily-decorated Marine Corps pilot who died last month when his combat jet crashed near a San Diego base during a training flight.

Major Andrew Mettler was piloting an F/A-18D Hornet when it went down at just before midnight on August 24 near Marine Corps Air Station Miramar.

That crash was the fifth Class-A aviation mishap – meaning damage totaling over $2million or fatality – in the current fiscal year.

It was the first involving a Marine Corps plane, according to Task & Purpose.