Final Pockets
Although some historians cite the League's defeat at Villalar as the end of Comunero movement, resistance did continue. The events of April 1521 effectively ended support for the Junta in the north, but Toledo, which had been at the rebellion's forefront since the start, became the new focal point. Padilla's wife, the formidable Maria Pacheco, and the highly martial Bishop of Zamora, assumed the mantle of leaders, and the town remained in revolt until February 1522, when it, and the rebellion, finally surrendered. Royal troops may have crushed the surviving pockets sooner had they not been called to the North of Spain, where the French had invaded Navarre.
The Aftermath
The crown's initial treatment of the rebels was harsh, but a General Pardon issued by Charles in 1522 covered all but 293 people; only 23 of these were executed. Indeed, the towns retained all their previous powers and privileges, but crown's victory was so great that it could demand concessions, including a greater willingness to grant the servicio. Additionally, the corregidores were also restored, although the crown did make greater efforts to monitor them.
Why the Rebellion Failed
The Revolt of the Comuneros dominated Castile for over eight months, effectively suspending royal power in the region. The major towns quickly formed a new, truly representative, body, established their own militia and made several key conquests, including the queen's residence and the regent's court. Yet, the Santa Junta failed to achieve victory, or even seriously threaten the Spanish inheritance of Charles V. Without the support of another possible monarch, the Junta either had to deal with Charles or change the constitution of Castile altogether, and this conflict paralysed the League. Additionally, the Junta couldn't count on full support from the northern towns, or any assistance from the southern ones.More importantly, complete success depended upon the co-operation of the grandees and their considerable military strength. Although much of the nobility shared the antipathy towards Charles that fuelled the rebellion, developments forced the grandees against the Comuneros. As the crown could do relatively little - and Charles did almost nothing - to halt the revolt, it was the grandees that ultimately defeated the Santa Junta.
In short, the Revolt of the Comuneros failed because of the fragmented and divisive nature of Spanish society and politics. Despite a 'common enemy', the towns themselves could not overcome their differences and self-interest, let alone form an alliance with their long-term rivals, the aristocracy. When the rebellion was crushed, it was not by people fighting for Charles, but by nobles fighting to safeguard themselves. Historians are left to argue whether events would have progressed differently had Joanna supported the Junta; we will never know.

