Human beings feel the burdens of conscience and its challenges to their personal and professional duties and responsibilities. Pip was wounded at the Trust's Irish estate in an incident where his co-worker was murdered; he feels the force of the religious obligation to continue work there. Members of the Trust struggle with their collective conscience with their ownership of the estate the subject of confused discussion, a dismal meeting with Irish MPs, and the assignment of Tom and Hannah (Pip's daughter) for an analysis conducted against the background of Home Rule and the cultural hatreds in 1896.

Albert Pirrip, Estella's stepson becomes a man without conscience. His youthful infidelity snapped his relationship with Elizabeth Fitzroy, now happily married with children to Timothy Egerton, a senior diplomat posted to London for a top-secret mission. Albert learns that Timothy has committed suicide in his office and decides to go to the funeral as a mark of respect. Elizabeth shares her distress with him, though Albert wants to revive their former relationship. He has become a person who sees the world through contracts and manipulations, despising the philanthropic impulse of the Trust. His marriage flounders when his wife Victoria confronts him about Elizabeth. Thereafter he consorts with prostitutes after his wife's rejections, and he contracts syphilis. Unable to face the depredations of the disease, his wife's anger and the loss of his children's love, he commits suicide,

Pip's son, Captain Malcolm Gargery, is in a liaison role at Port Elizabeth, South Africa as the Boer War gets under way. He shadows Emily Hobhouse in her famous enquiries into conditions in the concentration camps established for women and children. This convinces him that Kitchener's army has no conscience and he cannot be a part of it. Mr. Justice Hamish Macdonald, also struggles, but with conflicts between law and justice, on the execution of a mentally disturbed man, a case of bigamy and police methods of enquiry.

Elizabeth consults her friend's husband Sir Clarence Smythe MP on Timothy's suicide. Foreign Secretary Lord Salisbury allows Clarence to be informed that Timothy was in fact poisoned which has surprising ramifications. Clarence presents himself as a lover to Elizabeth which she deftly rejects and he sees that infidelity would test his conscience. She is also importuned by the Prince of Wales when she goes to the Palace to receive her husband's posthumous award but she refuses.

Tragedies leave parents with pangs of conscience, even where they deserve no blame. A magnificent elm tree at Numquam House is uprooted in a gale killing two of Victoria's nephews. This catastrophe brings Victoria into closer contact with John Eustace, the widowed young Vicar of All Hallows, but Pip's religious fervor is stimulated by the accident and the history of Numquam House as a center of tragedy. His visit to comfort the dead children's parents leads to a theological dispute but a later reconciliation between Vicar John and ex-Methodist preacher Pip. However, the status of women continues to be controversial in the upbringing of children, sexuality and the suffrage. In 1899 suffragism was a regular conversation at dinner parties, but for women the question of militancy in the face of male intransigence raised complex questions of conscience. Queen Victoria's death in January 1901 might perhaps be a turning-point.