[citation needed] James Hamilton, Earl of Arran, was appointed Regent and agreed to the demand of King Henry VIII of England that the infant Queen should marry his son Edward.

The English King Henry VIII, angered by the Scots reneging on the initial agreement for the royal marriage, made war on Scotland in 1544–1549, a period which the writer Sir Walter Scott later christened the "Rough Wooing".

[8] In response to the invasion Scotland looked to France for assistance, and on 16 June 1548 the first French troops arrived in Leith, soon to total 8,000 men commanded by André de Montalembert sieur d'Esse.

[6] From 1548 onwards work began fortifying the port of Leith initially with a bulwark at the Kirkgate and at the chapel by the harbour (later the site of the Citadel), perhaps designed by the Italian Migliorino Ubaldini.

In September 1559 she continued to improve the fortification at Leith and the island of Inchkeith with works which were probably designed by Lorenzo Pomarelli, an Italian architect and military engineer.

A group of noblemen, styling themselves the Lords of the Congregation, appointed themselves leaders of the anti-French, Protestant party, aligning themselves with John Knox and other religious reformers.

In 1559 the Lords of the Congregation gained control of most of central Scotland and entered Edinburgh, forcing Mary of Guise to retreat to Dunbar Castle.

[17] Châtellerault summoned other Scottish lords in October 1559, citing the French refortification of Leith: ...it is not unknawin how the Franchmen hes begun mair nor 20 dayis to fortifie the toun of Leyth, tending thairthrow to expell the inhabitantis thairoff and plant thame selffis, thair wyffis and bairnis thairintill suppressing the libertie of this realme.

[20] Landowners affected by the new fortification works were compensated, one merchant William Dawson was granted exemption from any future customs duties for the loss of his building in North Leith.

[22] In response to the situation, Elizabeth appointed the Duke of Norfolk to lead a diplomatic mission, and he met the Scots leaders to conclude the Treaty of Berwick.

[25] At the end of January 1560, an English fleet, under the command of William Wynter, arrived in the Firth of Forth, having sailed north from the naval base at Queenborough Castle in the Thames Estuary.

[5] On 2 February, a proclamation was issued in the name of the Queen of Scots to summon the men of Selkirk and Jedburgh to be ready to mobilise against the "wicked doings of the English ships" in Scottish waters, and the intended invasion of the Merse and East Lothian.

Considering the weather and difficulties of the road into Scotland, on 8 February 1559 Thomas Howard, Duke of Norfolk and Lord Grey de Wilton wrote to the Lords of Congregation from Newcastle; "we find greate difficultie of the cariadge of the same by land at this tyme of the yere, as well by reason of the deepe and foule wayes between Barwick and Lythe, as also that for such a number of cariadges and draught horses as the same doth require can not be had in time, and therefore we suppose the same must of necessity be transported by sea, and the number of footmen also appointed for this journey to be set on land as near unto Lythe as may be convenientlie.

[29] Camping for a night at Halidon Hill,[30] then at Dunglass and Lintonbriggs, the English army were at Prestongrange on 4 April where the lighter artillery pieces for the siege were landed from ships at Aitchison's Haven.

[35] Grey of Wilton set his camp at Restalrig village on 6 April 1560 and twice offered to parley with Mary of Guise and the French military commander Henri Cleutin, Sieur d'Oysel et Villeparisis via the English Berwick Pursuivant.

Five years earlier, Vaughan and James Croft had been imprisoned as supporters of Lady Jane Grey, and they subsequently took part in Wyatt's Rebellion.

According to a later chronicle, the History of the Estate of Scotland, the besiegers' guns were placed at the same distance of "twoe fflight shott" from South Leith church as Mount Pelham.

The French journal also mentions Pilrig as well as the entrenchment at Pelham, and a rumour that the newly arrived English great guns would be placed in the trenches on Hawkhill to the south.

John Lesley, Bishop of Ross, wrote that despite the bombardment, the French commanders and Father Andrew Leich celebrated Easter mass in South Leith Parish Church.

[58] The Diurnal of Occurrents records another attack on the completed Mount Pelham on 18 June by 300 French soldiers who were chased back to Leith by 30 English cavalry.

[61] The completed emplacements stretched for approximately 1 mile (1.6 km) around the fortified town, with six gun sites at a distance of around 500 yards (460 m) from the Leith ramparts.

[68] The accountant and victualler of Berwick, Sir Valentine Browne noted there were 1,688 men unable to serve, still on the payroll, hurt at the assault or at various other times, and now sick or dead.

According to Knox, Mary of Guise surveyed her victory from the fore-wall of Edinburgh Castle with some pleasure, comparing the English dead laid on the walls of Leith to fair tapestry, laid out to air in the sun: The Frenche, prowd of the victorie, strypit naikit all the slayne, and laid thair carcassis befoir the hot sune alang thair wall, quhair thay sufferit thame to lye ma dayis nor ane, unto the quhilk, quhen the Quene Regent luikit, for myrth sche happit and said, "Yonder are the fairest tapestrie that I ever saw, I wald that the haill feyldis that is betwix this place and yon war strewit with the same stuiffe.

[78] The French journal of the siege puts the story on 5 May, and says that Guise required ointment from one Baptiste in Leith, and the secret cipher on the back of the letter was "insert the notice of the English enterprise and other matters."

[80] An English secretary in Paris, John Somers or Sommer, managed make an alphabet or cipher key for some of the codes used by Guise and French diplomats.

[84] By 18 June 1560, after Mary of Guise had died, the French at Edinburgh Castle realised their cipher was in English hands, and they advised the Leith garrison to continue to use the code in letters that might be captured, to spread disinformation that would be advantageous in the ongoing peace negotiations.

Grey was worried about deserters "stealing" back into England, but he thought that with reinforcements he could take the town by storm, or enclose it and starve out the garrison, as there was already "great scarcity" within.

The 17th century writer John Hayward gave a description of famine in the town based on the account of an English prisoner in Leith called Scattergood.

[48] The total number of French evacuated from Scotland to Calais under William Winter's supervision was 3,613 men, 267 women, and 315 children—in all 4,195 with Lord Seton and the Bishop of Glasgow.

A ship scuttled by the French to block the harbour of Newhaven was floated off in September 1560 over two successive high tides by men working from small boats.