In 1641, a major rebellion broke out in Ireland, led by northern Catholics such as Sir Phelim O'Neill and Lord Maguire.
[3] During the Siege of Dublin, O'Farrell was routed by troops led by Lord Inchiquin while attempting to bring a relief convoy to the beleaguered garrison of Dundalk.
However, Waterford still had access to reinforcements from the west and up to 3,000 Irish soldiers (from the Confederate's Ulster Army) under General Richard Farrell were fed into the city in the course of a week.
Farrell, having been a successful officer in the Spanish army, was highly trained and experienced in siege warfare from battles in Flanders.
When Owen Roe died in 1649, O'Farrell was one of the candidates to replace him as commander of the Ulster Army, although he did not receive the post.