[2][10] Brennan is regarded by many as having brought stability to the diocese after the publication of the Ferns Report, in which 100 cases of clerical sexual abuse which occurred during the episcopacies of his predecessors, Brendan Comiskey and Donal Herlihy, were disclosed.

"[12]While the diocese insisted that weekly collections would not contribute towards redress for victims, it was estimated that €60,000 a year would need to be raised from parishioners over a 20-year period, with the alternative being to sell diocesan assets and properties including the bishop's house in Wexford, the seminary at St Peter's College and agricultural land.

Brennan participated in a meeting with Irish bishops, Pope Benedict XVI and senior members of the Roman Curia from 15 to 16 February 2010 to discuss the publication of the Ryan and Murphy reports in 2009.

In an interview on Morning Ireland on RTÉ Radio 1 on 17 February, he referred to the meeting as a "watershed moment" that would redefine the relationship between the Church and abuse victims, adding that a number of points regarding the mishandling of abuse cases by Church authorities were made by bishops "very honestly" in the presence of the Pope:[13]"The Holy Father has heard the many stories of Irish victims and I can also say they have been believed.

He was responding to criticism from victims groups who expressed disappointment at the failure of the talks to address several issues relating to the Church's handling of clerical sexual abuse cases.

[15] In accordance with canon law, Brennan submitted his episcopal resignation to the Dicastery for Bishops on his 75th birthday on 20 June 2020, but was expected to remain in the see until a successor was appointed.