The Spaniards and Tlaxcalans had been in Tenochtitlan for some two weeks when Cortes and his captains began to think of how to advance their purpose. They were guests of the Aztec State and at the same time hostages in the center of a city from which there would be no easy escape across the causeways and bridges. The only way to secure their plan of conquest was to capture the emperor Montezuma. Cortes and his captains asked for a royal audience and once admitted to the palace they quickly seized Montezuma. From the Aztec point of view this move was unimaginable, because the authority of Montezuma was paramount and he was to some extent a sacred person. Taken by surprise Montezuma had no choice but to submit or possibly lose his life. Due to the shock, he allowed himself to be conducted across the plaza to Axayacatl's palace where the Spaniards were quartered.

Despite being a hostage, Montezuma continued to conduct the affairs of state with his advisers and commanders from the guarded apartments. In the months that followed Montezuma developed a policy of appeasement while keeping up the civilities and expressions of affection with the Spanish troops. By early 1520, Montezuma had formally declared his vassalage to Charles V of Spain, and gave a hoard of treasure stored within the palace to the soldiers of Cortes. Cortes then asked for a place of Christian worship on the Great Pyramid. A crucifix was installed there with an image of the Virgin , and the Spanish leaders ascended the stair to kneel for mass. This sight caused tremendous anger among the common people of Tenochtitlan and the chieftains of the city began to take steps to rid the city of Cortes. Sensing this anger, Montezuma is said to have warned Cortes and asked him to leave or prepare for a possible confrontation.

Cortes was then called away by the Governor to answer for his previous rebellion. Upon returning to Tenochtitlan Cotes found the city deserted and silent. Long smothered resentment now burst forth in a furious cry for vengeance as squadrons of Aztec warriors assualted the Spaniards and Tlaxcalans in their palace stronghold. The Aztecs propelled stones and darts into the patio and the Spanish retaliated using cannons to clear the gate of charging enemy formations. At this point Montezuma was convinced to address his people and he proceeded to convince his people to pull back (This fact makes me sick to my stomach. Victory was eminent yet this weak ruler pulled his people back and in effect brought down his own empire). This was the last royal act of Montezuma. Soon after this, Montezuma's brother, Prince Cuitlahuac was elected as the new ruler and the attack was renewed. The humbled Montezuma again tried to calm his people but was met with jeers and rocks. Montezuma was stoned by his own people and fell to his death.

From the high platform the Aztec warriors continued to launch missiles. Cortes now became determined to take the Great Pyramid and personally led the attack. A fierce battle for the pyramid ensued, struggling men fell or were pitched over the edges of the pyramid. Superior weapons and battle discipline soon gained the upper hand and as the last group of Aztec warriors defended themselves, the Spaniards rushed to the chambers of the pyramid temples. As the troops set fire to the shrines, a column of smoke rose behind the victorious troops as they descended the steps of the pyramid. This was indeed a dreadful sight to the Aztec population, for in their practice of war, to capture and burn an enemy temple was the ultimate sign of victory. Despite his success, Cortes knew that his position was unstable and decided to escape from the city in the dark of the night. His army rushed to a causeway and laid down a portable bridge, but the vanguard soon reached the second gap before everyone had crossed the first. The portable bridge to had jammed and panic ensued as thousands of Aztec warriors began to appear in canoes along the sides of the narrow causeway. In the darkness, the Spaniards and Tlaxcalans pushed forward amid an unceasing hail of stones, darts, and arrows. The Spanish captains that reached safety were forced to return to help their comrades. The main body of the army made the crossing and regrouped to escape while the Aztecs turned their attention to captives. The Spanish refers to this battle as "Noche Triste" which translated means "Sad Night".

As the Spaniards regrouped over the next few months, Cortes visited the town of Tepeaca and made them his allies. By April 1521, the allied army departed once again for the Valley of Mexico. This time around their goal was to capture and overtake the great city of Tenochtitlan. Step by step Tenochtitlan was isolated. The three-pronged attempt met fierce resistance, and the Aztecs caused considerable damage as the fighting went back and forth. The allied force was tiny compared to that of the Aztecs and any gains made one day were lost the next. These slow and effective tactics gave the attackers the upper hand. Slowly the siege was tightened, while the city's population was gradually decimated by starvation, disease, and lack of fresh water. The Great Pyramid and the royal palaces were captured, as the Aztecs were trapped into the northern district of Tlatelolco. Cortes sent a message to Prince Cuahtemoc asking him to surrender. After 93 days of siege, on August 13, 1521, Cuauhtemoc was captured with his wife and chieftains as he tried to escape by canoe. Cuauhtemoc was taken to the rooftop where Cortes received his surrender with honor and respect. This surrender was in effect the end of the great Aztec Empire.