Archbishop Hebda said that after he arrived the archdiocese decided to cooperate with the county attorney "to try to make amends to those harmed and achieve justice for all in the broadest possible way."
"Cooperation seems to have been the right avenue for achieving a just resolution," he said.
Archbishop Hebda said the civil settlement with Choi's office commits to a course of action "that will keep kids as safe as possible."
"I am grateful that his office will hold us accountable," he said. "Today, we humbly acknowledge our past failures and look forward to continuing down that path to achieve those vital, common goals that together we all share."
The archbishop asked for prayers for sex abuse victims and their families, and for himself, and promised that he would pray for the faithful of the archdiocese.
Archbishop Emeritus Nienstedt also apologized for his response to sexual abuse allegations against priests in his archdiocese.
"Words cannot express the sorrow I feel for the victims and survivors of clergy sexual abuse, their families, their friends and our Catholic community," he said. "In particular, I am sorry for the way the archdiocese, under my leadership, addressed the allegations against Curtis Wehmeyer."
"As the archbishop, I should have asked more questions, I should have demanded more answers, and I should have insisted those within the archdiocesan administration at the time share more information with each other," he added. "I am sorry."
The legal agreement also made public a July 2014 memo from Father Dan Griffith, an archdiocesan priest who was a liaison to the lawyers conducting an independent investigation into Archbishop Nienstedt.
The memo concerned charges of criminal and sexual misconduct against the archbishop, and indicated that former apostolic nuncio to the U.S., Archbishop Carlo Maria Viganò, had prematurely ordered the end of the investigation and ordered destruction of evidence when he told two auxiliary bishops to destroy their objecting letter to him.
Archbishop Emeritus Nienstedt, who had approved the independent investigation, rejected all the sexual misconduct claims, and contended that the claims came from those who opposed his management decisions and his defense of Catholic teaching, especially on homosexuality.
(Story continues below)
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Father Griffith said in a statement that he stood by his memo and he has confidence in Archbishop Hebda, the New York Times reports.