Phillip II ordered the preparation of an expedition to conquer England. He ordered the gathering of a 35000 strong infantry and cavalry men army that would be transported from Dunkirk, through the English Channel, with flat bottom ships. They would be escorted and protected by a mighty fleet that was named the Invincible Armada. Lisbon was chosen to gather this famous fleet due to its strategic location and sheltering ability. The plan was simple: to dominate the sea in the English Channel in order to transport and land the army gathered in Dunkirk in complete security, and march later over London. The naval preparations that started in Lisbon, Cadiz, and Flanders would be delayed because of Drake's attack against the port of Cadiz, where he burnt 100 ships. It was in this incursion that the corsair attacked and destroyed the fortress located in Sagres, in the Algarve, before starting his pursuit of the India and America trade routes and ships. Upon his return to England, he passed in front of Lisbon; however, by the express order of Phillip II, the Marquis of Santa Cruz didn't leave to face him. The Invincible Armada finally gathered in the Tagus in early 1588 and left Lisbon on May 27. The storms and the English audacious attacks led to the failure of this mighty squadron which, according to Carlos Selvagem, "inspired more respect because of its apparatus than of its offensive power". With this setback, the Spanish naval power was destroyed, thus leading to the decadence of the House of Habsburg, to which Portugal was connected. The effects of this disaster were serious to Portugal. There is the example of the loss of Arzila, delivered by Phillip II to the Sultan of Morocco as a way of preventing a loan of 200 000 ducats that the contender Antonio tried to negotiate for war expenses because he was excited with the setbacks of Phillip II against England.

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