The reason he did this is all to do with the Marian Civil War. Halkerston had fought on the Catholic side and subsequently acted as an agent for various Catholic noblemen in attempts to re-establish Catholicism in Scotland. The Sinclairs were a prominent Catholic family and held out against Protestantism till around 1590. They were not major players in the war, but supplies were sent to the Marian side from Orkney by ship (presumably by the Sinclair's, who were the earls of Orkney) and captured by the King. This seems to be the motivation for attacking official ships coming back from Shetland and Orkney.
An excellent essay on Halkerston can be found here. This suggests a further ship was stolen from Peterhead. Some additional information on Halkerston's poetry can be found here.
Although the King called for Matthew Sinclair to be apprehended it appears he evaded capture and lived on until 27th June 1602 when he was set upon and murdered by a group of conspirators including his nephews Francis Sinclair of Uyea and Robert Sinclair; Robert’s servant John Lindsay; Adam Sinclair of Brew (my 6th great grandfather), John Bruce (servant to Adam Sinclair); John Sinclair (son of Laurence Sinclair of Goat) and another Laurence Sinclair (son of William Sinclair of Ustaness.
The murder trial was held before the Lawting Court at Scalloway on 16th August 1602 without the defendants present as they were fugitives. Found guilty their whole goods, lands and gear were forfeited. A trader from Bremen called Garth Hemlein was suspected of involvement, but acquitted.
According to the court documents as recorded in “Notes on Orkney and Zetland: illustrative of the history, antiquities, senery and customs of those islands” by Alexander Peterkin, Edinburgh 1822. Adam Sinclair (my 6th great grandfather) had fallen out with Matthew and paid his servant John Bruce to kill him. Following this, master and servant fled the island. The court’s exact judgement was that he was to be captured and beheaded as an example to others:
Quhairunto the Assyse taking long and mature deliberatioun, be the inspectioun of the chepturis of the law-buik, and practicks of the countrie in sic caices, and the haill premises found lawfullie provin, decernis the said Adam's haill moveabills, guids, and gere, with his haill heritabil landis and possessiouns, to be escheit, and himself beneist the countrie within the space of 15 dais, and gif he beis apprehendit thairaftir, to be tane to the Heiding-hill of Skalloway-Bankis, and thair his heid to be tane and strukin fra his bodie, in exampill of utheris.(The “law-buik” in question was still the law of Norway which was still in force at this time on Orkney and Shetland.)
It appears that the reason for the falling out of Matthew and Adam Sinclair may have been over the plundering of a Dutch wreck, Adam being indicted for this crime in the same session of the court:
In an action against Adam Sinclair of Brow for wrongous and violent intromission with goods of a broken Dutch ship, without leave of the owner, or any commission from my Lord his deputes, or the Foud of the parish; " the Assise taking this to consideration, and trying him to have committit great wrang and oppressioun thairinto, thai all in ane vote decernis the said Adam, with his haill moveabill guids and gere, in my Lordis will thairfoir, in exampill of utheris, reserving place to satisfy the partie."I hope to find out more about Matthew Sinclair and James Halkerston's piratical activities as I continue my research. Alas, due to Adam Sinclair going on the run my branch of the Sinclair family left behind what remained of their privilege to become poor fishermen and subsistence farmers.
Halkerston fled to Antwerp in 1573 to fight for the Dutch against the Spanish and apparently died penniless in London in 1615.