I haven't read the book so I can only comment in general. The Irish Confederation was an alliance of Irish Catholics during the seventeenth century. Their broad aim was for an Independent Ireland, but this took several forms. For some it was complete independence, for others it was about the independence of the Irish Crown, which had been subsumed under that of England. The history of the 'Irish Rebellion' during the 1640s is complex. Sometimes the Confederate forces fought against the English Royalist forces; at other times they formed an alliance with King Charles I against the Parliamentary forces (which caused a rift and a civil war within Ireland). For those wanting to know more, Wikipedia has an excellent article which gives the broad outline of events and people.