The issue of religion is a further source of difference between Anne and James; she, for example, had abstained from the Anglican communion at her coronation.
Anne has been brought up a Lutheran, but she may have discreetly converted to Catholicism at some point, a politically embarrassing scenario which alarms ministers of the Scottish Kirk and causes suspicion in Anglican England.
Queen Elizabeth had certainly been worried about the possibility and had sent messages to Anne warning her not to listen to papist counselors and requesting the names of anyone who had tried to convert her; Anne had replied that there was no need to name names because any such efforts had failed.
Anne has drawn criticism from the Kirk for keeping Henrietta Gordon, wife of the exiled Catholic George Gordon, Marquess of Huntly, as a confidante; after Huntly's return in 1596, the St. Andrews minister David Black had called Anne an atheist and remarked in a sermon that "the Queen of Scotland was a woman for whom, for fashion's sake, the clergy might pray but from whom no good could be hoped."
When former intelligence agent Sir Anthony Standen is discovered bringing Anne a rosary from Pope Clement VIII, James imprisons him in the Tower.
Anne protests her annoyance at the gift, but will eventually secure Standen's release after ten months.
James meanwhile, as a result of the various plots, had on February 19, 1604, denounced the Catholic Church .
Three days later he orders all Jesuits and all other Catholic priests to leave the country, and reimposes the collection of fines for recusancy.
It is currently considered unlikely that Sir Walter Raleigh had any culpability in the Main Plot; see the biography of Raleigh's prosecutor, Sir Edward Coke.
Raleigh is to remained in the tower until 1616.
While imprisoned, he will write many treatises and the first volume of The Historie of the World (London, 1628) about the ancient history of Greece and Rome.
His son Carew is conceived and born (1604) while Raleigh is legally "dead" and imprisoned in the tower.
