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Photo provided by Facebook -- Nate Cain, 49, resigned his post as warden of the Avoyelles Correctional Center in May.

Nate Cain, the eldest son of famous former Angola prison Warden Burl Cain, led a cover-up of a rape investigation last year at the Cottonport lockup where he was warden, according to an internal corrections department report.

The former Avoyelles Correctional Center warden also showed “inappropriate favoritism” toward the female guard accused of having sex with an inmate there, the investigation by the Department of Public Safety and Corrections concluded. Under the federal Prison Rape Elimination Act, sex between guards and prisoners is considered rape even if both parties say they consent.

The report was released in response to a public records request by The Advocate.

Nate Cain abruptly resigned last month at age 49 amid at least one internal probe by the corrections department and an investigation at the prison by the state Inspector General. Nate Cain’s lawyer, Jill Craft, has said her client and his wife, Tonia, 41, an administrator at the prison, both stepped down because of Nate Cain’s poor health.

But the 31-page investigative report — commissioned by Nate Cain’s brother-in-law, DPSC Chief of Operations Seth Smith, and carried out by Assistant Warden Ronald Moore — makes clear Cain was facing discipline, and possibly termination. It outlines a sordid relationship involving a guard with whom Nate Cain may have been romantically entangled, and sketches out a patchwork of lies and coercion by top officials in handling an allegation that could have meant — and could still bring — serious consequences for those involved.

In the end, the report concluded Nate Cain committed aggravated malfeasance and made false statements, but he was not punished because he resigned before the disciplinary process was complete, according to civil service guidelines, said corrections spokeswoman Natalie LaBorde.

The report says the conspiracy to tank the rape case also involved Nate Cain’s deputy warden, Paul Gaspard, who retired last month, as well as the prison’s chief investigator, Lt. Col. Beau Milligan, and his colleague, Maj. Randon Harrington, both of whom were fired last week. The guard accused in the rape, Lt. Brandy Dupuy, no longer works at the corrections department. Officials have not responded to questions about whether she was forced out or simply quit.

Craft, Nate and Tonia Cain’s attorney, said the report relies on rumors and insisted that Nate Cain followed policy in the rape investigation.

“Every witness who is interviewed repeatedly said that Nathan Cain said, ‘Do what you need to do,’ ” Craft said, adding the phrase meant Cain wanted a legitimate investigation.

Milligan’s attorney, Thomas Davenport, said his client is appealing his firing and is “innocent of all of these allegations.”

Calls and messages to Harrington and Gaspard were not returned. Dupuy said she would like to respond, but did not reply to further queries.

The departures from the Avoyelles Correctional Center come months after Burl Cain, once a towering force in the prison system who called corrections Secretary Jimmy LeBlanc his “very best friend,” abruptly announced last year he was stepping down after The Advocate revealed his business dealings with relatives and friends of inmates who got favorable treatment.

“Obviously, they’re just wanting to clean some house to get rid of the Cains, which is not something that my client is concerned with,” Milligan’s attorney said.

LaBorde did not respond to that claim.

‘Inappropriate relationship’

The report says the alleged trysts happened when the other guards were asleep.

Dupuy, whose shoulder was inked with tattoos of black birds and the words “Live Free,” the report said, kept her ear close to the door to make sure no one heard her late-night sex in the prison barbershop with a man serving 40 years for a sex offense. She sometimes brought the inmate, now 23, gifts of Xanax and ecstasy pills.

It was an “awfully risky” practice, in the words of Nate Cain — so risky that he doubted it could have happened, according to the report. The warden also found the inmate’s statement “too specific” in parts, such as the offender’s description of Dupuy’s undergarments, and therefore dubious.

The inmate told investigators that Dupuy had assured him she wasn’t worried. Cain was “her boy” and he “has her back.” Besides, according to the inmate’s statements to investigators, she told the offender that “she has something on Cain.”

The Advocate does not identify potential victims of sexual assault.

Sex between an inmate and a guard is not only illegal under federal law, it’s a potential security issue: The violent escape last year of two murderers from a prison in Dannemora, New York, began with an affair between one of the male offenders and a female guard.

Dupuy’s relationship with the inmate began to unravel when he sent an email Oct. 7 to a family member concerning Dupuy’s Facebook page. The department denied The Advocate’s requests to view the email.

The email was flagged by Troy Poret, a deputy warden at Avoyelles who has been in charge of the prison since Nate Cain’s departure. It sparked a review in which the inmate admitted to the sexual relationship, passed a polygraph test, and was placed into a single-man cell and written up for having an “inappropriate relationship with an employee.”

Days later, the inmate said, Harrington visited him in the cell and advised him it would be “in his best interest” to drop his claim of a sexual relationship with Dupuy. Harrington also said it was “what the wardens want,” and if the inmate refused, he might be sent to Angola’s notorious Camp J, where Louisiana’s most unruly offenders are kept.

According to Moore’s report, Harrington also said the inmate’s mother — who had separately been contacted by Dupuy — could face charges if he didn’t rescind his allegations.

The offender eventually signed a document dropping his claims, the report says.

But soon afterward, the inmate told Milligan, Harrington’s boss, that he had been coerced. The report alleges Milligan, a commissioned Avoyelles Parish Sheriff’s deputy, told the inmate that the Avoyelles Parish district attorney, a personal acquaintance, wouldn’t act on the allegations even if they got to him — an act the report describes as malfeasance.

Keeping things ‘in house’

While the inmate never had any direct contact with Nate Cain, it was Nate Cain who was behind the coercion, the report concluded.

When the warden was first told about the alleged sexual relationship with Dupuy, his “hands began shaking,” Moore wrote, citing statements he took from Poret and Milligan. Then Nate Cain “grabbed his chest and stated, ‘Y’all do what needs to be done for this.’ ”

It’s not clear why the news so discomfited the warden. But the report offers a possible explanation, saying that several employees interviewed by Moore believed Nate Cain and Dupuy had a romantic relationship. In the end, Moore wrote that while his review “did not prove or disprove the existence of a romantic relationship between Warden (Nate) Cain and Lt. Dupuy, the investigation revealed inappropriate favoritism shown to Lt. Dupuy by Warden (Nate) Cain.”

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Craft said the claims about Nate Cain’s affair are merely rumors and shouldn’t be believed.

“You’ve got the Department of Public Safety and Corrections, (its) trained law enforcement officers, who are essentially saying, ‘We think Nathan Cain may have had an affair with this woman, based on rumors.’ Those are their conclusions?” she said.

The report goes on to say that while Nate Cain initially told his subordinates to “do what needs to be done” to investigate, he soon took steps to undercut the probe.

Cain himself acknowledged to Moore that he cut short a polygraph on Dupuy — effectively quashing the rest of the investigation — because the offender was found to have lied in a separate instance.

The inmate had failed to disclose he was taking an antidepressant prior to his own polygraph, and Nate Cain determined that meant investigators had no probable cause to polygraph Dupuy.

A senior DPSC polygrapher later told Moore the medication issue with one person wasn’t a valid reason to stop a polygraph on another.

Craft questioned why polygraph exams were being used at all, noting they are inadmissible in court because they’re “unreliable.”

Nate Cain further torpedoed the probe by sending away Maj. Michael Vaughn, a seasoned investigator of the rape elimination law, from Angola whose help Poret had enlisted because Milligan and Harrington had never investigated a staff-on-offender rape case before, the report said.

But according to Moore’s investigation, Cain called a superior of Vaughn at Angola not long after the investigator arrived and complained that Vaughn was “too abrasive.” Vaughn’s colleague — himself a subordinate at the time of Nate Cain’s father, Burl — said he “ordered Vaughn to pack up his stuff and leave” the Avoyelles lockup.

When Moore asked Milligan if he ever considered contacting another seasoned investigator for advice about how to properly conduct the inquiry, Milligan said he would have been fired if he’d done so.

“(Nate) Cain likes to keep everything in house (and) not to let things get outside” of the prison, he said.

Moore also noted that Harrington worked with Nate Cain when both were stationed at Phelps Correctional Center, where both were lightly disciplined in the beating of an offender. Moore wrote that Harrington “has allegedly stated to other employees ... that he has fallen on a grenade for Warden (Nate) Cain before and would do it again.”

LeBlanc, the corrections secretary, said the statements Milligan and Harrington gave to Moore do not point to a culture of cover-ups at the Cottonport prison.

“The Moore report,” he said in an e-mailed statement, “included findings regarding an isolated event specifically involving Nate Cain and others and in no way states or implies that there is a systemic problem at the institution as a whole.”

‘They were afraid’

Moore’s investigation into a possible cover-up started on Feb. 26, almost five months after the initial probe cratered.

Smith, the No. 2 official in the state corrections department who’s also Nate Cain’s brother-in-law, asked Moore to look into whether the inmate’s rape complaint had been handled properly.

By then, the state Inspector General’s Office, an independent agency, already was reviewing the same issue, Smith told Moore.

The report points out that Smith was not informed of the extent of the allegations the first time around.

The document says that Nate Cain called Smith to alert him of the investigation, but didn’t fully explain the context of the probe to Smith, saying only that officers were probing an “inappropriate relationship” between a guard and an inmate, not an alleged sexual affair.

While Smith was on speakerphone, Vaughn tried to interject that the matter was a rape case, and Nate Cain angrily cut him off, the report says.

Vaughn later told Moore he felt the real reason he was sent away from the Avoyelles prison was that “they were afraid he might uncover whatever was going on.”

Moore’s report didn’t determine whether the alleged sex between Dupuy and the inmate really took place, noting that a separate investigation into the rape allegations is underway.

The corrections department has denied a request by The Advocate to provide the 38 exhibits, including emails and statements, that might support the allegations in Moore’s report, citing the potential role the documents could have in ongoing investigations.

“Where is all their alleged evidence, and why is that not available to anybody?” Craft said of the documents.

In the end, Moore found that Nate Cain, Gaspard, Milligan and Harrington had all committed “serious and egregious violations of Department Regulation and Employee Rules.”

Milligan and Harrington botched the rape investigation, the report said. And Gaspard, the deputy warden, was in charge of ensuring that the prison complied with the federal prison rape law, the report says, but he “failed to monitor any part of” the probe.

Nate Cain and Gaspard were not punished, since they retired before disciplinary proceedings were finished, said LaBorde, the corrections spokeswoman. No disciplinary action was instituted against Tonia Cain, LaBorde said.

“This man has worked in this line (of work) for a very long time. And to suggest that he is just as criminal as those in the prison, it’s uncanny. It’s remarkably pathetic. I find it offensive,” said Davenport, about his client, Milligan. “If there is any collusion, it’s not on the part of my client. I think it’s going to be on the part of the officials who want to clean house.”

Editor’s note: This story was changed on June 16 to clarify attorney Jill Craft’s remarks.

Advocate staff writer Gordon Russell contributed to this report.

Follow Kyle Whitfield on Twitter, @kyle_whitfield.​