Rural Rebellion and Failure
As the rebellion grew larger, cracks appeared in the alliance of towns as each had their own agenda. The pressure of supplying troops also began to tell. The rebellion spread into the countryside, where people directed their violence against the nobility as well as the king. This was a mistake, as the nobles who had been content to let the revolt carry on now reacted against the new threat. It was the nobles who exploited Charles to negotiate a settlement, and a noble led army which crushed the comuneros in battle.More Info: The Failure of the Comuneros
The revolt was effectively over after the Santa Junta was defeated in battle at Villalar in April 1521, although pockets remained until early 1522. The reaction of Charles wasnt harsh given the standards of the day, and the towns kept many of their privileges. However the Cortes was never to gain any further power and became a glorified bank for the king.
More Info: Aftermath of the Comunero Revolt
The Germania
Charles faced another rebellion which occurred at the same time as the Comunero Revolt, in a smaller and less financially important region of Spain. This was the Germania, born out of a militia created to fight Barbary pirates, a council which wanted to create a Venice like city state, and class anger as much as a dislike of Charles. The rebellion was crushed by the nobility without much crown help.More Info: History of the Germania Revolt
1522: Charles Returns
Charles returned to Spain in 1522 to find royal power restored. Over the next few years he worked to change the relationship between himself and the Spaniards, learning Castilian, marrying an Iberian woman and calling Spain the heart of his empire. The towns were bowed and could be reminded of what they had done if ever they opposed Charles, and the nobles had fought their way to a closer relationship with him.More Info: Charles' Return and Peace 1522 - 29

