It sounds straightforward enough: A missions agency faced with decades-old allegations of sexual abuse within its ranks hires an outside organization to investigate.

But add to that mix physically and emotionally scarred victims and dueling standards of proof, and the scenario becomes much more complex.

Godly Response to Abuse in the Christian Environment (GRACE) gained prominence in 2009 when New Tribes Mission (NTM) hired it to review sexual abuse claims. In November, it launched a similar third-party investigation for Bob Jones University. Now a Baptist missions agency has challenged the group's methods and terminated their relationship.

Nearly two years ago, the Association of Baptists for World Evangelism (ABWE) hired GRACE to investigate allegations that Donn Ketcham, a former missionary in Bangladesh, sexually abused missionary kids in the 1980s and that the agency had botched its handling of the claims.

But just weeks before the planned release of a final report, ABWE—whose board in 2011 fired its former president, Michael Loftis, and demanded the resignations of other top officials as the agency confronted "past mistakes"—announced it would work instead with a new firm.

ABWE raised concerns about GRACE's professionalism and investigative tactics and suggested that the investigators seemed intent on portraying the missions agency in a negative light.

"We began to realize that as trained prosecutors involved in doing investigations for a child advocacy ministry, their focus appeared to be on building a case rather than finding facts," Tony Beckett, ABWE's vice president of church relations, told CT.

Boz Tchividjian, GRACE's founder and executive director, countered in a point-by-point response that ABWE appeared "unwilling to have itself investigated" unless it controlled the investigation. He said that GRACE's team, which mostly consisted of pastors and trained clinical psychologists, used professional investigation methods in line with current best practices.

ABWE repeatedly refused to provide critical documents and other information, said Tchividjian, a former Florida child abuse prosecutor and grandson of Billy Graham. "When the institution controls the process, there's an inherent conflict of interest," he told CT.

ABWE said several witnesses voiced concerns that interviews by GRACE "were not conducted in a professional way or in complete independence and autonomy." Beckett said the witnesses had asked for confidentiality and thus were not available to CT.

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Reported victims, some reached by CT, expressed anger and disappointment with ABWE's decision to replace GRACE with a new firm, Professional Investigators International (PII).

"There is no hope for ABWE. They are absolutely wrong, and I am firmly convinced that they will face judgment for their actions," said the sister of one victim, who requested anonymity but provided a statement that she said her minor sister was forced to sign in 1989 confessing to a "physical relationship with Dr. Don (sic) Ketcham that transgressed God's Word and that was not pleasing to Him."

"[PII] promises complete confidentiality with their client, which is exactly what ABWE needed to survive this mess," said another victim who asked that her name be withheld. "So they have it, and the victims have nothing—least of all any hopes of a fair and transparent investigation."

Beckett said ABWE desires transparency and will release PII's final investigative report when it is completed.

Nita Zelenak, spokeswoman for NTM, said its working relationship with GRACE ended amicably and on schedule in 2010, after GRACE released its report on abuse at an NTM missionary school in Senegal in the 1980s.

Now three new investigations span decades of allegations in Brazil, Panama, and Bolivia—but NTM did not retain GRACE to conduct these interviews. Instead, NTM selected Pat Hendrix, who previously served as sexual misconduct ombudsman for the Presbyterian Church (USA), to coordinate its Independent Historic Abuse Review Team (IHART). The group is scheduled to release a report in March, as well as another by year's end.

"There were concerns about GRACE's process that came to light after the completion of their report on the [school]," she said. "NTM chose not to discuss those concerns publicly, but some of them mirror problems cited by ABWE."

Tchividjian said GRACE experienced "many of the same institutional self-protection obstacles" with NTM as with ABWE, but "never received any complaints." NTM adopted more than 95 percent of GRACE's final recommendations, he said.

In the late 1990s, the Christian Missionary Alliance became one of the first evangelical missions groups to face demands for accountability over such allegations of abuse. (It apologized and attempted to reconcile with victims in 1999). One of the highest-profile survivors: Wess Stafford, outgoing president of Compassion International, who authored a CT cover story on his abuse. Stafford declined comment to CT.

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The Child Safety Protection Network—a group of 50 mission agencies, faith-based NGOs, and international Christian schools that establishes best practices to prevent such abuse—declined comment to CT, which previously examined whether the rise of abuse allegations has contributed to the decline of attendance at boarding schools for missionary kids.

Beverly Shellrude Thompson, president of Missionary Kids Safety Net, which will host its first conference for survivors this April, said the conflict is predictable since such investigations involve decades-old events in locations outside the reach of American courts.

"For most victims, it's the only [investigation] they'll ever have. … It's the only court the alleged perpetrator will go through," she said. "Determining standards of proof and investigatory procedures [in such cases] is difficult. I am sympathetic."

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