As for the governance of the church, all but one of the Marian bishops refused to consecrate a new Archbishop of Canterbury (canon law from the 4th century required a minimum of three for consecration). Intent upon maintaining the three-fold ministry of deacon, priest and bishop in the apostolic succession, Matthew Parker, a Cambridge University don (lecturer), priest and former vice-chancellor of the university, was consecrated in December 1559 by four bishops. Two had been ordained using the 1550 Ordinal and two in the mid-1530s using the Roman Pontifical. All four had been consecrated by men in Roman Catholic orders. The church might be "reformed" in theology but there would be no break with the ancient institutional church in governance.
The Papal bull Regnans in Excelsis, issued on 25 February 1570 by Pope Pius V, declared "Elizabeth, the pretended Queen of England and the servant of crime" to be a heretic, released all of her subjects from any allegiance to her, and excommunicated any who obeyed her orders. The bull, written in Latin, is named from its incipit, the first three words of its text, which mean "ruling from on high" (a reference to God). Among the queen's alleged offences, it lists that "she has removed the royal Council, composed of the nobility of England, and has filled it with obscure men, being heretics."
When Mary I died in 1558, Elizabeth I succeeded to the throne. One of the most important concerns during Elizabeth's early reign was the question of which form the state religion would take. Communion with the Roman Catholic Church had been reinstated under Mary using the instrument of Royal Supremacy. Elizabeth relied primarily on her chief advisors, Sir William Cecil, as her Secretary of State, and Sir Nicholas Bacon, as Lord Keeper of the Great Seal, for direction on the matter. Many historians believe that William Cecil himself wrote the Church Settlement because it was simply the 1551–1552 version watered down.
Parliament was summoned in 1559 to consider a Reformation Bill and to recreate an independent Church of England. The drafted Reformation Bill defined Holy Communion in terms of Reformed Protestant theology, as opposed to the transubstantiation of the Roman Catholic Mass, included abuse of the Pope in the litany, and ordered that ministers should wear the surplice only and not other Roman Catholic vestments. It allowed priests to marry, banned images from churches, and confirmed Elizabeth as Supreme Governor of the Church of England.
The bill met heavy resistance in the House of Lords, as Roman Catholic bishops and lay peers opposed and voted against it. They reworked much of the bill, changed the proposed liturgy to allow for belief in the Real Presence of Christ in the Holy Communion, made allowance for the wearing of liturgical vestments, the celebration of the Communion in the customary place (altar or table against the east wall), and refused to grant Elizabeth the title of Supreme Head of the Church. Parliament was prorogued over Easter, and when it resumed, the government entered two new bills into the Houses; the Act of Supremacy and the Act of Uniformity. The Black Rubric of 1552 which permitted kneeling to receive communion out of reverence and not to imply the "real and essential" presence, was repealed at the express order of the Queen. Henceforth kneeling was customary and Real Presence implied without defining it with a doctrine such as transubstantiation. In 1662 the Rubric was restored but the words were changed to "corporal" to exclude the meaning that Christ was present physically in flesh and blood.