From this periodto the English invasion the history of Armagh exhibits a series of calamitous incidents either by hostile inroads or accidental fires.  It's annals, however, evince no further relation to the events of that momentous period than the fact of a synod of the Irish clergy having been held in it by Gelasius, in 1170, in which that assembly came to the conclusion that the foreign invasion and internal distractions of the country were a visitation of divine retribution, as a punishment for the inhuman practice of purchasing Englishmen from pirates and selling then as slaves ; and it was therefore decreed that every English captive should be liberated. 

The city suffered severely from the calamities consequent on the invasion of Edward Bruce, in 1315, during which the entire see was lamentably wasted, and the archbishop was reduced to a state of extreme destitution, by the reiterated incursions of the Scottish army. During the local wars in Ulster, at the close of the 15th and the beginning of the 16th centuries, this city was reduced to a state of great wretchedness; and in  the insurrection of Shane O'Nial or O'Neal, Lord Sussex, then lord-lieutenant, marched into Ulster to oppose him; and having attacked him successfully at Dundalk, forced him to retire upon Armagh, which the lord-lieutenant entered in Oct. 1557, and wasted with fire and sword, sparing only the cathedral. 

In 1566, O'Nial, to revenge himself on Archbishop Loftus, who had transmitted information of his hostile intentions to Government, even before the Irish chieftains and the lord deputy had preferred their complaint against him, resolved on a special expedition against this city, and on this occasion committed dreadful havoc, not even sparing the cathedral.  In the year 1575, Sydney, the lord-deputy, marched into Ulster against Turlogh O'Nial, and fixed his headquarters at Armagh, whither that chieftain, after some ineffectual negotiations through the agency of his wife, proceeded, and having surrendered himself, was permitted to return home without molestation.  In the short but sanguinary war carried on between the English Government and Hugh O'Nial, Earl of Tyrone, towards the close of the reign of Elizabeth, the Earl obtained possession of this place by stratagem; but unfavourable events in other parts soon obliged him to evacuate the place.  In the course of the same war, Armagh was again invested, in 1598, by this chieftain, who hoped to reduce it a second time by famine, but was baffled by the treachery of his illegitimate son, Con O'Nial, who, having deserted to the English, discovered a private road by which Sir Henry Bagnall, the British commander, was enabled to send in such a supply of men and provisions as completely frustrated the earl's efforts.  Soon after, the English were utterly defeated, and their commander killed, in a desperate attempt to force O'Nial entrenchment's, the immediate consequence of which was their evacuation of Armagh, which, however, was retaken in 1601, by Lord Mountjoy, who made it one of his principal positions in his Ulster expedition, and occupied it with a garrison of 900 men.  In the early part of the 17th century, a colony of Scottish Presbyterians settled here, from which it is supposed Scotch street, near the eastern entrance of the town, took its name.

At the commencement of the war in 1641, Armagh fell into the hands of Sir Phelim O'Nial, who, on being soon after forced to evacuate it, set fire to the cathedral, and put to death many of the inhabitants.  On the breaking out of the war between James II. and William, Prince of Orange, the Earl of Tyrconnel, then lord-lieutenant under the former sovereign, took the charter from the corporation, and placed a strong body of troops in the town; but they were surprised and disarmed by the people of the surrounding country, who had risen in favour of the new dynasty: the garrison was permitted to retreat without further injury to Louth, and Lord Blaney, having taken possession of the town, immediately proclaimed King William.  This nobleman, however, was soon afterwards compelled to evacuate it, and retreat with his forces to Londonderry, at that period the last refuge of the Protestants.  James, in his progress through the north to and from the siege of Derry, rested for a few days at Armagh, which he describes as having been pillaged by the enemy, and very inconvenient both for himself and his suite.  In 1690, Duke Schomberg took possession of it, and formed a depth of provisions here.