In Basel, the French Directory was relatively generous because it needed the Spanish navy, which was the third largest in the world. He returned to the traditional alliance of France and Spain against England, this started the alliance with Napoleon. This is the meaning of the San Ildefonso treaty (1796). Spain became an auxiliary of France, which forced him to enter the war the following year. In Europe, the English inflicted a severe defeat on the Spanish navy at Cape San Vicente (February 14, 1797); in America, they occupied the island of Trinidad, located in front of the mouth of the Orinoco and, therefore, an excellent base for smuggling. The internal situation was no better. The enlightened elite felt disappointed, if not persecuted; the most significant case is that of Jovellanos , upright and respected magistrate who, after a brief stint in the ministry, fell into disgrace and was banished to the provinces. The popular layers manifested an unrelenting hostility against Godoy. The court could not ignore the rise and violence of discontent. He sacrificed Godoy, who left the government, but I keep all the honors and emoluments accumulated over the last few years.
Although he had officially been removed from power, Godoy retained the confidence of the king, who did nothing without consulting him. Spain at that time gave the impression of playing the inglorious role of helping Napoleon's France, obsessed with the desire to destroy the power of England. Spain participated in the expedition that France planned to intimidate Portugal, an ally of England. On that occasion —the so-called orange war (February 1801)—Godoy acted as general in chief of the Spanish army. Determined to humiliate England, Napoleon conceived of two plans:invade her territory and ruin her trade; these projects are at the origin of the French intervention in Spain. The Spanish government had to put its navy at Napoleon's disposal. The French and Spanish squadrons met in Cádiz; when they tried to leave the port, the English admiral Nelson met them at Trafalgar (October 1805); On that occasion, Spain lost a large part of that navy to which it had devoted so much effort since the time of the Marquis of Ensenada. He destroyed both armadas.
Godoy agreed to participate in a new expedition to force Portugal to apply the continental blockade decreed by Napoleon against English products. He was all the more willing to do so as Napoleon gave him to understand that he would derive some personal advantage from her. In effect in October:1807, the French Emperor declared the House of Braganza dispossessed of its rights; Portugal was going to be dismembered and Godoy, Prince of the Algarves, would obtain sovereignty over the southern part of Portuguese territory. In application of the Treaty of Fontainebleau (October 22, 1807), French troops began to cross Spain, heading to Portugal; other French troops seemed to want to head towards Andalusia. Godoy then suspected that Napoleon was thinking of occupying all of Spain and advised Carlos IV to leave the capital and go to Seville; from there, if the situation worsened, the royal family could embark for America, as the Portuguese royal family had just done.
Carlos IV followed Godoy's advice, but could not go beyond Aranjuez. Indeed, for months, discontent had increased against Godoy, whom he blamed for all the misfortunes of the nation and who was attributed an excessive personal ambition; in January 1807 he had received new honors:the title of Grand Admiral of Spain and of the Indies, the title of serene highness that assimilated him to a member of the royal family. These facts pushed his opponents to group around the crown prince Don Fernando; it was about putting him on the throne of Spain instead of his father, Carlos IV. A first conspiracy failed in El Escorial (October 1807). But the second was more successful, in Aranjuez, on March 17, 1808. Two days later, Carlos IV had to sacrifice Godoy and remove him from all his titles, but the crowd was not satisfied. Carlos IV had no choice but to abdicate in favor of his son on March 19. Ferdinand VII set out to reign, but the presence of the French army in Spain made Napoleon become the arbiter of the crisis in which the Spanish royal house was mired. Napoleon lured Charles IV and his son to Bayonne, and forced both abdications. In this way he imposed his brother José I on the throne of Spain .