Season 03 Episode 01

Sidney meets the new archdeacon, Gabriel Atubo, who notes that his predecessor was removed under some controversy and embarrassment and asks whether Sidney can be relied on to rebuild trust in the church. Sidney assures him he can. That night Sidney dances with Amanda Hopkins while Geordie and Cathy sit nearby, the distance between them plain. Afterwards Amanda tells Sidney that he is a good man, and that this is what stops them from getting any further.

Sidney finds the vicarage door open and a live crow in a closed room. He is telephoned by Geordie, because a body has been found in the Round Church in Cambridge. Dr Terrence Atwell, who ran a soup kitchen for the homeless, lies dead, and water spills from his mouth when the body is turned. The caretaker, Patrick Harland, says he found him. A homeless man, Jerry, who had been outside the church all night, repeats the name Bonnie and nothing else, and a second dead crow is found in Atwell's bedroom. An anonymous caller reaches Sidney more than once, will not speak, and describes how birds die.

Margaret Ward finds that Atwell and a woman named Ivy Franklin, a former matron at Dapple Oak, a home for the mentally feeble, both worked at the same institution, and that Ivy died a few months earlier, with Sidney conducting her funeral. Sidney and Geordie visit Ivy's daughter Hilary, who is nursing her ill father and who found a bird in the house. Jerry is then found holding Grace at the vicarage, and Sidney nearly strangles him before he calms; Jerry says he saw someone drown Atwell. Ivy Franklin's body is exhumed with Hilary's permission and a doll is found in the coffin. Leonard, who has been staying with Hilary, catches her burning a letter addressed to Sidney; she says it was left at the funeral, that it contained accusations against her mother, and that her mother burned her with a poker, leaving the scars on her arm. She says Dr Atwell told her to keep the letter secret.

At the institution the woman in charge, Veronica Stone, denies knowing anyone named Bonnie and lets them see the paperwork. A patient, Andrew, tells Sidney that Bonnie liked birds because they could fly away. Geordie finds coded documents and Margaret breaks the code, establishing that Bonnie's surname begins with H. Sidney receives a call threatening Grace, goes to Amanda's cottage, and is attacked in the bathroom by Patrick Harland, who tries to drown him while Amanda fights him off. Harland's room at the church is full of caged birds, and at the institution he is found trying to drown Veronica Stone.

Patrick Harland, the church caretaker, drowned Dr Atwell and had earlier killed Ivy Franklin, as revenge for the death of his daughter Bonnie, who was killed at Dapple Oak, where staff disciplined children by holding their heads under water and neither Atwell nor Ivy would tell him where the child was buried. Veronica Stone is taken away in a police car, and with Andrew's help the grave is found and Bonnie is given a headstone. Sidney says a prayer for the institution's dead. Sidney also tells Amanda that they cannot stop Guy Hopkins from seeing Grace, and the two of them take the baby to him, and Guy breaks down, holds his daughter and admits he has made a mess of things. Sidney walks out of Guy's house and takes up smoking again.

The episode is the strongest of Series 3 and the darkest of the run, because the crime is a man killing the people who would not tell him where his child was buried while the institution that killed her is left standing. The birds are the whole visual scheme, from the crow in the vicarage to the caged birds in Harland's room, and the episode is unusual in the series for making the killer's motive entirely sympathetic while his method is drowning. Sidney being attacked in the same way he is investigating, in Amanda's bathroom with Grace in the house, is the point at which the case reaches the people he is trying to keep out of it.