At first Morton was not unfavourable to the Catholics owing to the disputes that arose between himself and the preachers about the re-establishment of the episcopal form of government， but later on he adopted a policy of violent opposition to the old religion. Some of the priests were put to death； others were arrested or banished； a list of Catholics including Beaton the Archbishop of Glasgow， Leslie Bishop of Ross， and Chisholm Bishop of Dunblane was drawn up for proscription， and steps were taken to suppress Catholic holidays and to remove from the churches everything that called to mind Catholic devotions.
In 1578 the young king demanded Morton's resignation. A council of twelve was appointed in his place， at the head of which stood the Earls of Argyll and Atholl. Elizabeth was annoyed at the fall of her minion， and took no pains to conceal her annoyance from the young king. It looked as if friendly relations between the two courts might be broken， and the Catholic party both at home and on the Continent were filled with new hopes. In 1579 Esmé Stuart， Lord d'Aubigny， a nephew of the former Earl of Lennox， arrived from France， where he had been educated as a Catholic. He was welcomed at court by the king and created Earl of Lennox. James fell completely under his sway， though the preachers regarded d'Aubigny as a Catholic spy. Regardless of Elizabeth's friendship， James was induced to open communications with his mother， and when the Earl of Morton rose in rebellion against such a policy he was arrested and put to death (1582). Though apparently Lennox made profession of accepting the established religion in Scotland， he was endeavouring secretly to bring about an understanding between Mary and her son， to secure the release of the former from captivity， and to assist the Catholic cause. The preachers took alarm at the sudden and unexpected increase of Popery. "Before this French court came to Scotland，" said Walter Belcanqual in one of his sermons in 1580 "there were either few or none that durst avow themselves Papists， neither yet publicly in the country， neither in the reformed cities， neither in the king's palace. But since that time， not only begin the Papists within the realm to lift up their heads， but also our Scottish Papists that were outside the realm swarm home from all places like locusts， and have taken such hardihood unto them that not only have they access to the French court， but also in the king's palace， in the particular sessions of our kirks， and general assemblies thereof， durst plainly avow their Papistry， and impugn the truth， both against the laws of the realm and discipline of the Church， contrary to all practice that we have had before."[36]
The members of the General Assembly， annoyed at the attempt of the king to support the episcopal system of government， were determined to remove Lennox， whom they regarded as an emissary of Rome. Elizabeth's agents， too， were busy stirring up discontent. A plot formed by Ruthven Earl of Gowrie， the Earl of Mar， and others， for the capture of the king， was carried out successfully during a visit paid by James to Ruthven's castle at Gowrie (The Gowrie Plot). He was seized and lodged safely in Stirling. The Earl of Arran who attempted to rescue his sovereign was made prisoner， and Lennox was obliged to flee to France (1582).
For a time Melville and the preachers， who gloried in Gowrie's successful machinations， held the king in bondage. The General Assembly of 1582 expressed its approval of what had been done，[37] and renewed its attacks upon the episcopal system. James， however， succeeded in making his escape from confinement； the Earl of Arran was recalled to court； Ruthven was declared a traitor and was beheaded， and the other conspirators were obliged to make their escape to England. James entered into close correspondence with some of the Catholic powers abroad， and even went so far as to appeal to the Pope for assistance against the enemies who surrounded him (1584). For a time it seemed as if a great Catholic reaction was about to set in.
Priests who had escaped from England were labouring with success in the Scottish mission-fields； a few Jesuits had arrived from the Continent， and France， Spain， and the Pope were in correspondence regarding the assistance that might be given to James and his mother.
But the spies of Elizabeth soon obtained knowledge of what was in contemplation. France and Spain were too jealous of one another to undertake an armed expedition， without which success was impossible.
Negotiations were opened up with a view of detaching James from the Catholic party， and of inspiring him with distrust for his mother. As he was always more anxious to secure his accession to the English throne than to defend either his mother's life or her religion， he succumbed completely to English influence.