The year is 1988, and psychiatrist Tom Allen is still recovering from the death of his wife and an ill-fated love affair with Alice. When a boy at the local Catholic school goes missing, questions are asked of many in the community. Two popular clergy members – Father Andrassi and Brother Warner – launch a desperate search to find the missing boy. But the church is also facing internal moral problems, and Tom is called in to counsel a number of the priests dealing with a range of personal issues. As Cardinal Neville prepares to retire, his time in the position is celebrated by state MP Margaret Wallace, but a battle has also begun for the top job in the Sydney archdiocese.

Quaid decides to commence an investigation of his own into the allegations made by Margaret and Brendan. Brendan infiltrates Tom’s world when he meets his son, David. Elliot becomes the target of new unwanted attention.

A body is discovered, and a cryptic note suggests the death is not an accident. Father Andrassi becomes a new client of Tom’s. A meeting between Quaid and Brendan causes Quaid to question the secrets being kept within his church.

Tom takes his concerns about the ongoing case to Bishop McNallly but later finds that his house has been broken into. Meanwhile, another boy goes missing.

In the wake of the investigation, Tom discovers his own past is also under public scrutiny and his life is being threatened from unknown quarters. Bishop Quaid reveals the results of his own investigation to Margaret, and Alice learns the truth.

Tom confronts Bishop McNally and threatens to leak the results of his investigation beyond the confines of the institutional church. Margaret, Tom and Quaid attempt to end the Church's corruption and internal concealment of it, but they could risk their personal relationships and professional careers as they do so.