The Lord Deputy & Council
Late Medieval Period
At the start of the 16th Century, the Dublin government formally claimed jurisdiction over the whole island. In some cases, governors were able to obtain recognition by Gaelic chiefs of the King’s rights in Ireland. In practice however, the English government in Ireland was limited to the main areas under Anglo-English influence; the Pale and surrounding lordships including, in particular lands held by Kildare, Ormond, Butler and others.
Viceroys were styled Justiciar traditionally, Deputy, or Lord Lieutenant. The office of chief governor of Ireland existed under various names from (Chief) justiciar (13th–14th centuries); (King’s) lieutenant (14th–16th century) and  (Lord) Deputy The unofficial term Viceroy was also common.
In the earlier years, there were frequent long vacancies, during which a Lord Deputy or Lord Justice would act as chief governor. Many governors were deputies or deputy lieutenants. The governor was advised by an Irish Council. He was head of the civil administration and the military commanders.
Poynings Law
At various times in the late 15th century the Crown reserved its powers of appointment thereby asserting greater control over the Irish administration.The period saw further reductions in the governor’s powers. A statute of 1494 provided that judges and financial officials held tenure during the Crown’s pleasure are only. Exceptions were licensed.
The infamous Ponying’s’ law in 1494  required license to hold parliament and introduce bills. It effectively subordinated the Irish parliament to the English privy council.
The Irish Council
The governor was advised by an Irish Privy Council. He was head of the civil administration and the military commanders. He served for a fixed term, were paid a fixed salary and might receive other Irish revenues. Significant offices were often been granted for life in some cases, including ones carrying a place on the council.
Seven chief ministers and councillors who held office by virtue of other office were the core of the Council. It included lawyers, military captains, royal nominees, close confidants of the governors and others. The Inner Council or Privy Council was established in 1520. This was an inner council advising the governor on daily administration. The Privy Council with Chancellor acting as President might undertake business in the deputy’s absence. The larger council included local leading magnates.
The Council was assisted by clerks drawn from the Chancery. The governor’s private seal was kept by a secretary and also acted as the second royal seal. It was used to authenticate the more important administrative documents such as royal grants and commissions. In  1494 a separate writing office was created separate from Chancery for use by the government. The Chancery Department developed as a court of equity in the late 15th century. Warrants for the Chancellor were filed in Chancery. The Chancery kept roles. Grants and commissions were to be enrolled.
Henry VIII King of Ireland
For most of the 15th and early 16ht centuries and before, the Lord Deputyship was effectively granted to Anglo-Norman magnates. The Earls of Kildare, Butlers or Dukes of Ormand had almost continuously held the role of Lord Deputy. Latterly the Earl of Kildare monopolised the lord deputyship. This reflected practical considerations of economy.
Following Kildare’s failed rebellion, the position changed fundamentally. Henry VIII sought to bring the Irish magnets under his control by the regrant of English titles. He admitted native Irish lords into the Irish parliament , in return for their submission to him as King of Ireland.
Ireland became an independent kingdom under the English Crown after 1541. It was distinct from England notwithstanding sharing the Crown. The power in Ireland t lay not with the Parliament, but with the Lord Deputy of Ireland, who was nominated by the King, The Parliament met only when called by the Lord Deputy when he wanted to pass new laws or raise new taxes.
After the rebellion of 1534, the governor was almost always English born with limited exception. Most governors were lord deputies or deputy lieutenants. Apart from the long vice royalties of two Dukes of Ormond from 1643 to 1713, no one of Irish birth was appointed thereafter as Lord Deputy. The important posts within the Irish administration were reserved to English natives.
Positions in the church, judicial bench and civil administration were routinely conferred on persons of English and later British birth. This contrasted markedly with Scotland where its own native ecclesiastical system and judicial system survived and were staffed locally.
Stuart Era
The accession of James VI of Scotland as James I of England on the death of his cousin Elizabeth I provided a parallel for the relationship. This Stuarts were independently kings of Scotland, England and Wales and Ireland; the so-called three kingdoms.
The 17th century commenced with the defeat of Hugh  O’Neill (Earl of Tyrone/ Gaelic Chief)  at the end of the nine-year war in 1603 and the subsequent flight of the Earls in 1607. Tyrone’s rebellion had been lost after the Battle of Kinsale and a scorched earth  policy followed with subsequent defeats for O’Neill and O’Donnell. The dying  Queen Elizabeth seeing O’Neill in surrender at the end of the war authorised the Lord Deputy to offer term to the rebels.
Evolution of Irish Council
The nature of the Irish Council changed over time. The council did not involve into a comprehensive executive. The council intermediated on draft bills from London and those emanating from the Irish parliament. Most councillors were members of one or other house of parliament and were somewhat politicised.
The number of members of the council varied. At the beginning of the 18th century, it was at 56. However, attendance was relatively low, and business was undertaken by relatively few. The effectiveness of the  council varied considerably. At times it was relatively unwieldy and inefficient.
Viceroy
The Lords Deputy / Lord Lieutent employed auxiliaries to assist with the business of government. Much was delegated. From 1660s onwards, the lords lieutenant hired undertakers and surrogates to manage the affairs of the king. A function of the undertakers was to smooth the  passage of bills through parliament. Tensions rose as these surrogates and appointees sought greater powers and spoils of office in order to reward  their followers.
In the absence of the viceroy/lord lieutenant, notables in Dublin were requisitioned to act as lords justices. A troika comprising the lord chancellor, speaker of the house and the primate (Archbishop of Armagh) of the church of Ireland played a key role in government. Other Irish nobles and notables were included from time to time.
By the early 18th century, the viceroy’s role was both ceremonial and administrative. They held court and made their impact through the scale and style of their hospitality.
Lords lieutenant / viceroy might be accompanied by an entourage. The viceroys struck strategic alliances with persons of influence in Ireland. Some  viceroys were relatively weak. Petitions were made to the Crown over the head of the viceroy given his subservience and relatively weak position.
Many Viceroys  came to Ireland only every second year and then only for the duration of the parliamentary sessions typically up to six months. Deputies were appointed. Ormond preferred to spend time in England where he doubled as Lord’s Stewart of Charles II household. He left Ireland to his sons Ossory and Arran.