Queen Elizabeth's intentions were to capitalise upon Spain's temporary weakness at sea after the successful repulsion of the Spanish Armada and to compel Philip II to sue for peace. The expedition had three objectives: to burn the Spanish Atlantic fleet, to make a landing at Lisbon and raise a revolt there against Philip II (Philip I of Portugal), and then to continue west and establish a permanent base in the Azores. A further aim was to seize the Spanish treasure fleet as it returned from America to Cádiz, although this depended largely on the success of the Azores campaign.
The strategic objective of the military expedition was to break the trade embargo imposed across the Portuguese empire, which included Brazil and the East Indies, among other areas, and trading posts in India and China. By securing an allegiance with the Portuguese crown, Elizabeth hoped to curb Spanish Habsburg power in Europe and to free up the trade routes to these possessions.
This was a difficult proposition, because the domestic aristocracy and clergy of Portugal had accepted Philip as their King in 1581 at the Cortes of Tomar. The pretender to the throne, António, Prior of Crato — last surviving heir of the House of Aviz — failed to establish an effective government in exile in the Azores, and turned to the English for support. But he was not a charismatic figure, and with his cause compromised by his illegitimacy, he faced an opponent with perhaps the better claim, in the eyes of the Portuguese nobles of the Cortes, Catherine, Duchess of Braganza.
The complex politics were not the only drawback for the enterprise. Like its Spanish predecessor, the English expedition suffered from overly optimistic planning, based on hopes of repeating Drake's successful raid on Cadiz in 1587. A contradiction lay between the separate plans, each of which was ambitious in its own right, but the most pressing need was the destruction of the Spanish Atlantic fleet lying at port in Corunna, San Sebastián and Santander along the northern coast of Spain, as directly ordered by the Queen.
The expedition was floated as a joint stock company, with capital of about £80,000 — one quarter to come from the Queen, and one eighth from the Dutch, the balance to be made up by various noblemen, merchants and guilds. Concerns over logistics and adverse weather delayed the departure of the fleet, and confusion grew as it waited in port. The Dutch failed to supply their promised warships, a third of the victuals had already been consumed, and the number of veteran soldiers was only 1,800 while the ranks of volunteers had increased the planned contingent of troops from 10,000 to 19,000. The fleet also lacked siege guns and cavalry — items that had been lavishly laid-on in the Spanish Armada expedition of the previous year — which raises serious doubts about the intentions of those in charge of the preparations.
When the fleet sailed it was made up of six royal galleons, 60 English armed merchantmen, 60 Dutch flyboats and about 20 pinnaces. In addition to the troops, there were 4,000 sailors and 1,500 officers and gentlemen adventurers. Drake assigned his vessels to five squadrons, led respectively by himself in the Revenge, Sir John Norreys in the Nonpareil, Norreys' brother Edward in the Foresight, Thomas Fenner in the Dreadnought, and Roger Williams in the Swiftsure. Also sailing with them — against the Queen's express orders — was the Earl of Essex.
Most of the ships lost in Philip II's expedition of 1588 had been armed merchantmen, while the core of the armada — the galleons of the Spanish navy's Atlantic fleet — survived their voyage home and docked in Spain's Atlantic ports for a refit, where they lay for months, vulnerable to attack.
Unforeseen delays and a fear of becoming embayed in the Bay of Biscay led Drake to bypass Santander, where most of this refitting was underway, and attack Corunna in Galicia instead. Norreys took the lower town, killed around 500 Spaniards and plundered the wine cellars located there whilst Drake destroyed 13 merchant ships in the harbour. For the next two weeks the wind blew westerly, and while waiting for a change the English occupied themselves in a siege of Corunna's fortified upper town. A pair of Spanish galleys managed to slip past the English fleet and repeatedly resupply the defenders, and at length, with a favourable wind returning, the English abandoned the siege, having lost four captains and several hundred troops in the fighting, along with 3,000 other personnel in 24 of the transports, including many of the Dutch who found reasons to return to England or put into La Rochelle. Those who remained then turned their attention, first to Puente del Burgo, where Norreys won a modest victory, then to Lisbon.
Lisbon was rumoured to be guarded by a disaffected garrison, but whilst the English were fruitlessly besieging Corunna, the Spanish had spent a fortnight shoring up Portugal's military defences. When Norreys invested Lisbon, the expected uprising was not forthcoming and little was achieved. Drake did take the opportunity on June 30th of seizing a fleet of 20 French and 60 Hanseatic ships which had broken the English blockade on trade with Spain by sailing all around the north of Scotland, only to fetch up before the English cannon in the mouth of the Tagus. This seizure, notes R. B. Wernham, 'dealt a useful blow to Spanish preparations', but later required a publicly printed justification, a Declaration of Causes, from the Queen's own printer, as, without booty, she and her fellow English investors faced considerable losses.
The English dealt a further blow to Spanish naval preparations and food supplies by destroying the Lisbon granaries, but despite the bravado of Essex, who thrust a sword in at the gates of the city with a challenge to the defenders, the English could not take the city without artillery, neither did they receive substantial support from the Portuguese. The expected uprising failed to occur, in part because of the absence of Drake, the land and naval forces having divided and lost contact after the landing at Peniche (in Portugal), and the defenders would not risk battle.
Essex received orders from Elizabeth to return to court, along with a refusal to send reinforcements or a siege train, the queen having no desire to carry the main burden of a land war in Portugal. It was therefore decided to concentrate on the third aim of the expedition - the establishment of a permanent military base in the Azores. However, by this point the campaign had taken its toll. Drake's forces had initially caught the Spanish authorities off guard, but Spain had now marshaled her defences, and the English expedition's strength was wearing down, and suffering increasingly from disease. Two armed merchantmen were caught off Lisbon by nine Spanish galleys, commanded by Alonso de Bazán. One of them, the William, was saved by HMS Revenge after being abandoned by her crew, but the ship did not have enough manpower aboard her to sail away after the battle and had to be scuttled to prevent her falling into the hands of the Spanish again. The other vessel was engulfed in flames after a fight, and sunk, her commander Captain Minshaw being lost with the ship. Further damage was sustained when one of three boats carrying William's complement was lost with all hands after being attacked by the Spanish warships.
With the aim of assailing the Azores becoming increasingly out of the question, Drake made a final attempt to retrieve the mission. At this point, most its men were out of action, with only 2000 still fit to be mustered. Stormy weather had also damaged a number of its ships. Whilst Norreys sailed for home with the sick and wounded, Drake took his pick of what was left and set out with 20 ships to hunt for the Spanish treasure fleet. Whilst laying in wait for it his naval force was struck by another heavy storm which left him unable to continue, and whilst raiding and plundering Porto Santo in Madeira in compensation his flagship the Revenge sprang a leak through storm damage and almost foundered as she led the remainder of the fleet home to Plymouth.
Without counting the 18 launches destroyed or captured at Corunna and Lisbon, the English fleet lost about 40 ships. Fourteen of these were lost directly to the actions of Spanish naval forces: three at Corunna, six were lost to actions led by Padilla, three to Bazán and two to Aramburu. The rest were lost to a stormy sea as the fleet made its return voyage to England. The outbreak of disease on board the vessels was also transmitted to the port town populations in England on its return. None of the campaign's aims had been accomplished, and for a number of years this expedition's results discouraged further joint-stock adventures on such a scale.
The English expeditionary force had sustained a heavy loss of ships, troops and resources, but only brought back 150 captured cannon and £30,000 of plunder, along with the indecisive damage that it had inflicted to the Spanish forces in the fighting. Another indirect minor strategic benefit was, perhaps, a temporary disruption to Spanish military shipping activity, and the diversion of Spanish imperial resources that might have contributed to a mutiny by troops under the command of Parma in Flanders that August.
With the opportunity to strike a decisive blow against the weakened Spanish navy lost, the failure of the expedition depleted the financial resources of England's treasury, which had been carefully restored during the long reign of Elizabeth I. The Anglo-Spanish war was financially costly to both of its protagonists, and the Spanish Empire - which was also fighting France and the United Provinces at the same time, would be compelled in financial distress to default on its debt repayments in 1596 following another raid by the English on Cadiz. In 1595 the Spanish counter-attacked the English mainland at the Battle of Cornwall. In 1596 and 1597 two more armadas, substantially weaker than the great one she had issued in 1588, were sent by Spain against England, but both were scattered by storms on route. However the failure of the English expedition of 1589 marked an ebbing point in the Anglo-Spanish war, and the conflict wound down with diminishing military actions, until a peace was agreed between the two powers on the signing of the Treaty of London in 1604.