Let's start off with João III. He was the son of Manuel I of Portugal and Maria of Aragon. His mother was a daughter of King Ferdinand II of Aragon and Isabella of Castile. So João was a direct descendant of the King of Portugal, the King of Aragon, and the Queen of Castile. His father Manuel I is important as all eventual claims would trace back to him.

João III married his cousin, Cathrine of Austria, who was also a granddaughter of Ferdinand II and Isabella. Let's get used to that. The Avis family is basically done branching at this point

João III's sons had a tendency to die off young. His fourth son, João Manuel, married Joanna of Spain. She was his first cousin in both the paternal and maternal lines. That's how closely related the Spanish and Portuguese courts were at the time. João Manuel managed to impregnate his bride, shortly before dying of consumption at the ripe old age of 16, in early 1554. Eighteen days later his son Sebastian was born and became heir.

No one is sure what João Manuel or his brothers died from. It's called consumption in the sources. But everything from tuberculosis to diabetes has been suggested. He was the last of his siblings to pass. His older sister, Maria of Portugal, had been married to Phillip II of Spain. But she died shortly after giving birth to Don Carlos. Remember what I said about the family tree not branching? There's near constant interweaving of the Spanish and Portuguese families in both directions.

João III then died at the ripe old age of 55 in 1557 leaving his grandson Sebastian the crown.

Sebastian was raised by his grandmother Queen Catherine (João III's wife). His mother Joanna was acting as Regent of Spain for Charles V and then Phillip II, and apparently never saw her son after about 1556 or so. Catherine and Cardinal Henrique o Casto (the Chaste) were Sebastian's regents. Henrique was João III's younger brother.

Thing went well for Sebastian for a while. He came to his majority, but even before that was involved in court affairs. His "reign" was mostly a good one for couple of decades. In 1578 he crossed to Morocco to press some Portuguese claims in the area and died in battle at the ripe old age of 20. Well this was a problem. Sebastian never married and had no known children. He had been an only child. His aunt had one son, Don Carlos with Phillip II of Spain. But Don Carlos had already died. His only heir was his great-uncle, the 66 year old Henrique the Chaste. So Henrique became king of Portugal. Henrique asked to be released from his vows, but the pope refused. So Henrique remained chaste and died without an heir two years later. Phillip II of Spain immediately made a claim on the throne of Portugal. He was the grandson of Manuel I, nephew (and son in law) of João III, and uncle to Sebastian twice over, once by being his mother's brother and once by being his aunt's husband. There were at least two other claimants. Both of whom were also Manuel I's grandchildren. But Phillip II had an army. So Phillip II of Spain also became Phillip I of Portugal. I'll call him Phillip II/I from now on.

The Portuguese court did get some concessions. This was to be a personal union only; Portugal was not to be annexed. They were also to retain their own legal system and administrative system. In practice Phillip couldn't be in both places at the same time. He stayed in Madrid; Spain was by far the richer and more powerful of the kingdoms. So he was represented by a viceroy in Lisbon. The whole system provided a lot of independence and in most matters the Viceroy and the Council of State in Lisbon practically ruled the country. Portugal maintained its own legal code, its own courts, its own army and navy, even its own inquisition. Under Phillip II/I, Portugal ran as more or less a separate kingdom.

His son Phillip III/II however did not like this hands off approach. He tried in a number of ways to bring Portugal under the direct rule of Madrid. The Portuguese hadn't seen much in the way of benefits of being part of the Spanish empire. They saw increased taxes to pay for Spanish adventures in Europe. But they didn't see a lot flowing back. In fact a lot of their problems like their wars with the Dutch were a direct result of being attached to Spain. From their point of view he couldn't even keep part of his kingdoms (the Dutch) from attacking them. Now he was replacing Portuguese nobility with Spanish nobility, and Portuguese law with Spanish law? That was too much and the Portuguese launched the Restoration War to break the union.

João of Bragança had a viable claim to the throne, his grandmother and grandfather had both been grandchildren of Manuel I. Catherine of Guimarães had even been one of Phillip II's rival claimants. He became João IV. Spain was fighting the 30 year war, as well as facing other rebellions. It was a relatively easy but long rebellion for the Portuguese. Neither Philip III nor João IV would live to see the end of it, as it took 28 years of occasional fighting before Spain accepted Portuguese independence.

So it's important to distinguish between personal union and national union. Portugal was part of Phillip II/I's and Phillip III/II's domains. But Portugal wasn't ever part of Spain. When Phillip III/II tried to change that, the Portuguese rebelled. The Spanish kind of ruled Portugal. The Phillips were "Spanish" kings after all. But, as I've shown, there was plenty of Portuguese blood running in their veins as well. The Viceroy in Lisbon was generally "Spanish" also, but he was generally a Spaniard with Portuguese ties and relatives. The rest of the Lisbon court was truly Portuguese. So while the Portuguese king lived in Madrid during the Iberian Union he still was a separate legal entity. He was king of Spain and king of Portugal, two separate entities . He wasn't king of Spain and Portugal, a combined single entity.