Queen Elizabeth finally removed any Catholic pretensions in England. King James, long time King in Scotland, was brought up a not very happy Presbyterian but there was always a swirl of Catholic dissension in and around his court. This stemmed from a certain very small band of Scottish nobles’ loyalty to his mother Mary (Queen of Scots) and her rigid Catholicism. His minimal complaint, as King of Scotland, to the execution of his mother by Elizabeth, Queen of England, was an indication of his attitude towards Rome (and, presumably, to his mother). Mary was next in line to the English throne as a cousin of Elizabeth, who was unmarried and childless. James, the only non-Catholic of his siblings, became the presumptive successor. His desire to unite England and Scotland under his rule was, obviously, a powerful factor in maintaining a good relationship with Queen Elizabeth.
With the help of key nobles, James ruled Scotland as an absolute monarch. Not something he would be able to do in England, which has a very independent minded parliament.
On Mary’s death, James became King of England and Scotland. On his succession to the English throne, he tried to reduce the tensions in England. Tensions between old stock Catholic nobles, elements of the clergy still steeped in Catholic fervour and the protestant mainstream. Guy Fawkes destroyed that attempt. King James inherited the Church of England. With that, the inseparability of church and state. He was, after all, King, by divine right. Unfortunately, he inherited a Puritan movement that evolved under Elizabeth after the break from Rome. This movement always wanted to purify England’s new religion of all vestiges of Catholic influence. The pomp and ceremony of the Church, the catechism, the hierarchical structure and transferred traditions were equivalent to that of the secular nobility. The nobility and the Church were critically important components of a national institution under James’ absolute authority. He saw this purification (or Puritan) movement to be a threat to this national institution; therefore, to him and his authority as its head.
Within the Puritan movement there were those that wanted to purify the Church from within and then there were the separatists who wanted to separate from the Church to form their own fellowship, where each congregation was an independent community with its own elected leadership. Of most concern to James was an undercurrent commitment among the Puritans that Church and State should become entirely disconnected.
This movement gathered momentum. The response by the authorities was mixed. In the extreme case, with the separatists being persecuted and eventually fleeing the country, was an indication of the way a consistent and aggressive response evolved. There was a worry that the inherent community leadership that comes from disaffected parish clergy would turn whole communities against the institution of the Church of England and therefore against the authority of the King.