The Charlie Norwood Veterans Affairs Medical Center in Augusta, Ga., was a hospital with systemic failures.

Its gastrointestinal clinic was so overwhelmed and mismanaged that close to 5,000 referrals for endoscopies were delayed, auditors found, resulting in the deaths of three cancer patients in 2011 and 2012, hospital officials acknowledged in published reports.

Veterans complained of long wait times for other specialty care. Top management was in upheaval after resignations, firings and unfilled vacancies; directors cycled through, with the last departure leaving a vacancy for months.

[VA manager indicted on 50 counts of falsifying medical records of veterans waiting for care]

And when a scandal in Phoenix, Ariz., last year revealed that VA employees were manipulating wait times to hide long delays for patients, Augusta became one of 111 medical centers that federal investigators flagged for further review. Schedulers there told investigators they felt pressured to put appointment dates in the system earlier than the real ones, which were later on the calendar and exceeded the reasonable time a veteran should wait to see a doctor.

Amid the turmoil, a program analyst in charge of making sure veterans got appointments with outside specialists tried to solve the problems by pretending they didn’t exist, prosecutors alleged Friday when they charged Cathedral Henderson with ordering his staff to improperly close out more than 2,700 consults for outside care.

[VA removes manager at center of wait-times scandal]

Henderson, 50, a GS-12 in charge of revenue and billing and chief of “purchase care” for the Augusta medical center, pleaded not guilty last Friday to 50 counts of falsifying medical records. His indictment marks the first criminal prosecution in a scandal so serious it cost VA Secretary Eric Shinseki his job.

Unlike the six senior executives across the VA system who have been fired or retired after they lied about patient wait times, Henderson is a mid-level employee whose salary is $89,032. His lawyer says his client was acting under pressure from supervisors.

“There was an issue with consults, and he was asked to do something about it,” attorney Keith Johnson of Augusta said Monday. A  memo from VA headquarters had instructed local hospitals to close out all requests for outside care. VA “knew delays in care was an issue,” Johnson said, adding, “There was pressure applied to certain staff” to make the delays go away.

Prosecutors are not interpreting Henderson’s motives as generously.

Henderson “falsely declared the consults to have been completed or refused by the patients, when in truth and fact, as Henderson then well knew, the consults were still pending and unresolved, and the veteran patients were still waiting for the authorized medical consults,” the indictment charges, describing Henderson’s alleged actions over five days in February 2014.

VA officials said Monday they have proposed disciplinary action related to data manipulation or patient care against more than 187 employees nationwide. But they are all administrative, not criminal actions. It’s unclear what tipped the scale for Henderson.

Ray Kostromin, a primary care physician and whistleblower who worked at the  Charlie Norwood Medical Center for 11 years until his firing in 2013 after complaining about delays in care, recalled that referrals to outside specialists were exploding as the demand for care grew and hiring did not keep pace.

“We enrolled way more patients than we could take,” Kostromin said Monday. “They got entirely overwhelmed.” But money was tight, and managers hesitated to send too many patients to  outside specialists, he said. “The idea was, if your department is saving money you look good, so slow down the referrals.” Kostromin now practices at St. Francis Hospital in Columbus, Ga.

About 45,000 veterans in Georgia and South Carolina use the Augusta medical center, a 470-bed tertiary care teaching hospital with an operating budget of about $360 million.

Henderson was not a clinician. He was in charge of making sure outside doctors were paid. Part of his duties involved handing and managing consults. An Army veteran, he transferred to an administrative job in VA’s Atlanta office last year “because he needed a new environment,” his lawyer said.

“We just want people to understand he’s always been a soldier helping other soldiers,” Johnson said. “He’s a mid-level employee.”

The turmoil in Augusta was first investigated by the House Committee on Veterans Affairs, which held hearings in 2012 into wait time manipulation and delays at VA medical centers in Augusta, Columbia, S.C., and Dallas.

The Henderson case was brought to prosecutors by the VA inspector general’s office, which completed an investigation into delays in care in Augusta last fall. The investigation has not been publicly released at the request of the U.S. Attorney’s office, Catherine Gromek, a spokeswoman for the inspector general, said.