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 Queen Elizabeth's instructions to Howard of Effingham and Essex may be briefly summarised. The generals were advised that the armament had been originally collected because of the prevalence of reports that Spain was preparing a greater Armada than that of 1588 to invade England, and to aid the Irish rebels. The reports had turned out to be exaggerated. Moreover, the Spanish fleet had been scattered, partly for the pursuit of Drake and partly for the reinforcement of the Indies. But there was still danger that the Irish rebels might be assisted, and that might best be prevented by the capture or destruction of "some good number" of the King of Spain's ships in his ports. The duties of the generals would, therefore, be to discover the strength, whereabouts, and designs of the Spanish navy, and the nature and quantity of stores collected in Spain for purposes of aggression over sea; to destroy any vessels intended for Ireland, the Narrow Seas, or Calais, to generally injure the naval power of Spain, to avoid the unnecessary hazarding of ships and men, to take undefended towns, especially if they should be understood to contain treasure; not to injure non-combatants, and to preserve all booty for her majesty's disposal. The two generals were to be assisted by a council of five, composed of Lord Thomas Howard, Sir Walter Ralegh, Sir Francis Vere, Sir Conyers Clifford, and Sir George Carew; and the proceedings of the generals and council were to be from time to time recorded for the queen's information by Anthony Ashley, one of the clerks of her Privy Council, who would accompany the fleet for the purpose. If, after the attainment of the main objects of the expedition, the generals should learn of the home-coming of any rich Spanish carracks from the Indies, they might exercise their discretion as to effecting their capture; but the fleet was not to be kept abroad longer than needful.

Before the sailing of the expedition, the queen's attitude towards it, and especially towards Essex, changed; and, almost at the last moment, the two leaders received letters of recall. These were withdrawn only upon the urgent remonstrances of Lord Thomas Howard, Sir Francis Vere, and other subordinate officers.