In 1641 the Irish rose in rebellion and in Ulster the Planters fled to the protection of Derry's Walls. The then Mayor, James Vaughan, wrote to London outlining the plight of the overcrowded city and requested more arms, munitions and supplies. It was only in such dangerous times that the years of neglect by the Planters struck home. In response to the crisis the London Companies dispatched four ships to Derry with provisions and arms to withstand the semi-siege conditions.
The defence of the city and hinterland was organised by several army officers who formed a 'League of Captains'. They expelled all disloyal Irish inhabitants, cleared open ground outside the Walls and divided the city into defensive zones. Repairs to the Walls were carried out and at various times the captains led sorties against the rebels into the nearby counties of Tyrone and Donegal. Because of these measures the city itself was never actually attacked during the insurrection of 1641/42.
Derry was again besieged in 1649, this time by forces loyal to King Charles I during the English Civil War. Although many battles occurred in the surrounding countryside during the 20 week siege, no attempt was made to breach the Walls. Sir Charles Coote, the Governor who held Derry for the English Parliament, obtained the help of Owen Roe O'Neill, the Irish Chieftain, to force the Royalist forces to retreat.
Neither this attack nor the one in 1641 were comparable to the Great Siege to follow in 1689. In the earlier attacks the enemy did not bombard the city or attempt to breach the Walls. Sufficient supplies also reached the garrison, enabling the defenders to resist any attempts to starve them into submission. But in 1689 true siege conditions prevailed.