The next twenty years were occupied with the strife of Kirk and King,
whence arose "all the cumber of Scotland" till 1689. The preachers, led
by the learned and turbulent Andrew Melville, had an ever-present terror
of a restoration of Catholicism, the creed of a number of the nobles and
of an unknown proportion of the people. The Reformation of 1559-1560 had
been met by no Catholic resistance; we might suppose that the enormous
majority of the people were Protestants, though the reverse has been
asserted. But whatever the theological preferences of the country may
have been, the justifiable fear of practical annexation by France had
overpowered all other considerations. By 1580 it does not seem that
there was any good reason for the Protestant nervousness, even if some
northern counties and northern and Border peers preferred Catholicism.
The king himself, a firm believer in his own theological learning and
acuteness, was thoroughly Protestant.

But the preachers would scarcely allow him to remain a Protestant. Their
claims, as formulated by Andrew Melville, were inconsistent with the
right of the State to be mistress in her own house. In a General
Assembly at Glasgow (1581) Presbyteries were established; Episcopacy was
condemned; the Kirk claimed for herself a separate jurisdiction,
uninvadable by the State. Elizabeth, though for State reasons she
usually backed the Presbyterians against James, also warned him of "a
sect of dangerous consequence, which would have no king but a
presbytery." The Kirk, with her sword of excommunication, and with the
inspired violence of the political sermons and prayers, invaded the
secular authority whenever and wherever she pleased, and supported the
preachers in their claims to be tried first, when accused of treasonable
libels, in their own ecclesiastical courts. These were certain to acquit
them.