Andrews, his name appearing in the books of the college of St. Salvator for the session 1 Oct. 1563 to July 1564. He was boarded with John Rutherford, the principal of his college (ib. pp. 91-5). On 20 Dec. 1563 his mother died, and in the inventory of debts due by her is a sum of 18l. (Scots) to John Rutherford for her son's board (ib. p. 93). In the address to the 'Godly and Christian Reader' prefixed to his work on ' Revelation,' Napier states that, while at St. Andrews, he, 'on the one part, contracted a loving familiarity with a certain gentleman, a papist, and on the other part, was attentive to the sermons of that worthy man of God, Master Christopher Goodman [q. v.], teaching upon the Apocalypse.' He 'was so moved,' he continues, 'in admiration against the blindness of papists that could not most evidently see their seven-hilled city of Rome painted out there so lively by St. John as the mother of all spiritual whoredom, that not only bursted [he] out in continual reasoning against [his] said familiar, but also from thenceforth [he] determined with [himself] by the assistance of Gods spirit to employ [his] study and diligence to search out the remanent mysteries of that holy book.' The absence of his name from the list of determinants for 1566, or of masters of arts for 1568, makes it probable that after one or perhaps two sessions Napier was sent abroad to prosecute his studies; Mackenzie (Scots Writers, iii. 519) says he stayed for some years in the Low Countries, France, and Italy; but nothing definite is known. By 1571 Napier had returned home. On 24 Oct. 1571 his uncle, Adam Bothwell, now commendator of Holyrood House as well as bishop of Orkney, assigned to Sir Archibald and his sons, John and Francis, the teinds of Merchiston for nineteen years (Memoirs, p. 129), and, immediately after, negotiations began for John's marriage with Elizabeth, daughter of Sir James Stirling of Keir. In December 1571 a contract was entered into by the respective fathers, Sir Archibald ap-parently undertaking to infeft his son in the baronies of Edenbellie-Napier and Merchiston, and Sir James agreeing to pay Sir Archibald three thousand merks in name of tocher. Other deeds, dated 16 and 23 Feb. following, are in the Stirling and Napier charter chests; and on 2 April 1572 a deed was signed at Merchiston by John Napier and Elizabeth Stirling, preliminary to their marriage (Stirling of Keir, p. 43; Memoirs, p. 130) After some delays due to the political disturbances in which Napier's father was involved, a royal charter, on 8 Oct. 1572, granted to Napier and his future wife, in conjunct fee, the lands of Edenbellie, Gartnes, while Napier also received 'the lands of Merchiston with its tower and the Pultrielands; half the lands of Ardewnan, &c., half the lands of Rusky, Thorn, &c., with the house of Barnisdale; the third of the lands of Calziemuck ; and the lands of Auchinlesh.' The life-rent of all the lands save those in conjunct fee was reserved to Sir Archibald and his wife.
The couple being thus provided for, the marriage followed, and Napier and his wife settled on their property. A castle, beautifully situated on the banks of the Endrick, was built at Gartnes, with garden, orchard, and suitable offices; it was completed in 1574, as appears from a sculptured stone bearing that date, still preserved in a wall of one of the buildings of an adjacent mill. Two sundials from the castle have been recently taken to Helensburgh, and these are now almost the sole remnants of Napier's home. On the opposite side of the Endrick was a lint mill, and the old 'Statistical Account of Scotland ' (xvi. 107) records that the clack of this mill greatly disturbed Napier, and that he would sometimes desire the miller to stop the mill so that the train of his ideas might not be interrupted. His residence at Gartnes extended from 1573 to 1608, when the death of his father put him in possession of Merchiston Castle. Towards the end of 1579, after bearing two children, his wife died, and he subsequently married Agnes, daughter of Sir James Chisholm of Cromlix, Perthshire.
The political activity of his father-in-law, Sir James Chisholm, involved Napier in some anxieties. In February 1592-3 the conspiracy known as 'the Spanish Blanks' was discovered, and Chisholm, 'the king's master of the household,' was deeply implicated, along with the popish earls Angus, Huntly, and Erroll. The king, disinclined to proceed to extremities, desired that the conspirators should keep out of the way for a time. With this view, apparently, a bond of caution in 5,000l. (Scots) was signed, on 28 July and 3 Aug. 1593, by John Napier and another, that Chisholm, 'during his absence furth the realm, conform to his majesty's licence, shall do nothing to hurt his majesty, the realm, or the true religion' (Reg. Privy Council, v. 610). Chisholm and the earls, however, remained in the country. Accordingly, a small deputation of commissioners of the church followed the king to Jedburgh in October, and urged their speedy trial and punishment. One of the deputies was, according to Rymer (Foedera, 1715, xvi. 223-5), 'the laird of Markiston younger,' that is John Napier,
