First Part

After his abdication as Emperor of the Holy Roman Empire of the German Nation, Karl retires to the sanctuary of the San Jerónimo de Yuste monastery, where he wishes to spend his twilight years. Suddenly, the voice of God exhorts him to take responsibility for his actions as his Last Judgement. He calls for his confessor, the young monk Juan de Regla, in order that he may give an account of his life. First of all, he remembers his mother:
Juana, known as the mad woman, could not accept that her husband was truly dead. She gave Karl an apple, which he realised contained a worm. 

Karl tries, together with Juan, to interpret the symbolic meaning of the picture: Karl was appointed Kaiser and his enemies came from within, from his own empire. Karl subsequently thinks back to the Diet of Worms, where he met Martin Luther:
The reformer criticised the Pope in front of the congregated Diet. The clerics condemned him as a heretic and rebel. 

Karl justifies to his confessor why he forbade Luther’s preachings, despite the reformer’s theses against the Pope. Although Juan demands that Karl delve further into the depths of his conscience, Karl remembers another situation, namely the Battle of Pavia:
Gunfire was exchanged in Italy between Karl V’s Habsburg troops and the soldiers of Francis I, the king of France. The Kaiser emerged victorious from the battle and took his French rival as prisoner to Madrid. From his cell, Francis I petitioned Soliman, the Ottoman ruler, for help against Karl V. 

With reference to gold from America, Juan criticises Karl’s use of it to fight his wars:
Pizarro, after plundering gold from the southern and central American regions in the name of the Spanish flag, returned home to Seville. He and his men were not, however, prepared to share their spoils with Karl V’s empire. 

Karl condemns Pizarro’s rage and explains to Juan that he needs the gold to pay his soldiers’ wages. He also laments the fact that peace with Francis I is simply not possible.
Spanish women fell for the imprisoned Francis I – one of them was Eleonore, Karl V’s sister. The Kaiser fulfilled his sister’s wish and gave her to Francis as his wife, with Burgundy as a dowry. Upon his release, Francis declared the marriage null and void. Karl V appealed to Francis I to take care of Eleonore. Due to lack of regular payment, the German men-at-arms decided to conquer and loot Rome. 

Karl thinks back to the victory over the Ottomans at the Battle of Tunis and how he subsequently returned to Madrid to see his wife Isabella die. While the mourners sing a requiem for Isabella, four allegorical spirits plague Karl. He breaks down, and Juan calls for the Kaiser’s personal physician.

Second Part

Immersed in his visions, Karl fails to notice how the Jesuit Francisco Borgia exchanges information about his condition with Juan and Eleonore.
Luther spoke of the Reformation and its consequences. He had doubts about his work, but still explained that his deeds were necessary for a true faith in God.

Eleonore describes how she suffered at the Parisian court. Karl awakes and recalls the memory of the victorious Battle of Mühlberg:
After Karl V’s victory over the Protestants, the Kaiser prophesied that everybody would live together peacefully in a vast Christian empire. The Germans, however, rejected the decreed Catholicism and wanted to fight for their freedom. They prepared for a counter attack. Karl V narrowly escaped capture in Innsbruck. 
After the choir pronounced the end of Karl V’s empire, Soliman discussed the ebbing of Karl V’s power with an astrologer. It made Soliman very pleased to know that there was no one unified power in Europe anymore, and that the people were fighting against each other. Karl V fled from Innsbruck to Vienna where he voluntarily gave up his throne to his brother Ferdinand.

In his hour of death, Francisco Borgia, Eleonore and Juan are standing by Karl’s side. Four clocks indicate the expired lifetime of the Kaiser. While Juan asks whether Karl could have acted differently, Juan compels a dying Karl to show remorse for his actions. After uttering the words “Forever! To God! This is the time! Jesus!”, Karl dies, and Francisco Borgia says that an era has died with him. Juan replies, “His work is incomplete.”