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.