Morton had warning from Lord Robert Stewart, Mary's half-brother, to fly the country, for Sir James Balfour, with his information, had landed.

On December 31, 1580, Captain Stewart accused Morton, in presence of the Council, of complicity in Darnley's murder.

He was put in ward; Elizabeth threatened war; the preachers stormed against Lennox; a plot to murder him (a Douglas plot) and to seize James was discovered; Randolph, who now represented Elizabeth, was fired at, and fled to Berwick; James Stewart was created Earl of Arran.

In March 1581 the king and Lennox tried to propitiate the preachers by signing a negative Covenant against Rome, later made into a precedent for the famous Covenant of 1638.

On June 1 Morton was tried for guilty foreknowledge of Darnley's death.