On his return home, Sempill found new and worse troubles awaiting him. It happened that of the lands conferred upon Mary Livingston on her marriage some portion lay near one of Morton's estates. Not only had the Queen's gift been made by a special grant under the Great and Privy Seals, but the charter of infeofment had also been ratified by a further Act of Parliament in 1567, when it was found that the proposal to annul the forfeiture of George Earl of Huntly would affect it. It seemed difficult, therefore, to find even a legal flaw that would avail to deprive the Sempills of their lands and afford the Regent an opportunity of appropriating them to himself. He was probably too powerful, however, to care greatly for the justice of his plea. He brought the matter before the Court of Session, urging that the gift made by the Queen to Mary Livingston and her husband was null and void, on the ground that it was illegal to alienate the lands of the Crown. It was in vain that Sempill brought forward the deed of gift under the Great and Privy Seals, the judges would not allow his plea. Thereupon Sempill burst into a violent passion, declaring that if he lost his suit, it would cost him his life as well. Whiteford of Milntoune, a near relative of Sempill's, who was with him at the time, likewise allowed his temper to get the better of his discretion, and exclaimed "that Nero was but a dwarf compared to Morton". This remark, all the more stinging that it was looked upon as a sneer at the Regent's low stature, was never forgiven. Not long after the conclusion of the lawsuit, both Sempill and Whiteford were thrown into prison on a charge "of having conspired against the Regent's life, and of having laid in wait by the Kirk, within the Kirkland of Paisley, to have shot him, in the month of January, 1575, at the instigation of the Lords Claud and John Hamilton". After having been detained in prison till 1577, John Sempill was brought up for trial on this capital charge. His alleged crime being of such a nature that it was probably found impossible to prove it by the testimony of witnesses, he was put to the torture of the boot, with which he had been threatened on a former occasion. By this means sufficient was extorted from him to give at least a semblance of justice to the sentence of death which was passed on him. In consideration of this confession, however, the sentence was not carried out. Ultimately he was set at liberty and restored to his family. His health had completely broken down under the terrible ordeal through which he had gone, and he only lingered on till the 25th of April, 1579.