The Council was the powerful overseer of Spain's colonial empire, being responsible for government, administration, justice, taxes, war and religion.
This increased the travel time, typically to two or three months, when a fast ship, unescorted, could make the trip in three weeks.
Upon his arrival, Peralta reviewed the cases and suspended the death sentences given the sons of Cortés.
The Council proposed to the king that he send a special commission to the colony to investigate the situation and bring actions against guilty parties, up to and including the removal of the viceroy.
Commissioner Jarava died on the voyage, on July 18, 1567, one day after reaching Grand Canary.
The first decision of the commission was to construct a jail, "in the manner of those of the Santo Officio [Inquisition]", to imprison the principal accused, including Baltasar de Aguilar Cervantes and Luis Cortés.
He was condemned to ten years in the galleys, forfeiture of his property, and perpetual exile from the Indies.
Muñoz remained in Mexico City in accordance with his instructions from the king, to continue as interim governor of the colony until the arrival of a new viceroy.
Before Carrillo embarked from the port of Veracruz, however, a ship arrived carrying instructions ordering both commissioners to return to Spain and leaving the government in charge of the Audiencia.
Muñoz has been accused of dealing too harshly with the conspirators, and indeed King Philip II was said to be displeased with his severity.