The generals in Brittany prevented the rural armed groups from coalescing and taking control of the region. At the end of April 1793 republican control had been re-established, despite the fact that those opposing it remained in general totally hidden, sometimes concealed underground, most often in wooded areas or isolated villages, benefiting from the support of the peasants, whether voluntary or forced. A certain number of Bretons or insurgents from Maine and Anjou traveled to the south of the Loire, joining one of the Catholic armies being set up. After July 1793 complex confrontations between Girondins and Montagnards split the revolutionary camp even further: some of the defeated Girondins defected to the counter-revolution, the most famous of these being Puisaye, who entered into negotiations with various groups of resisters and succeeded in being named general-in-chief of the chouans at the end of the year (Hutt 1983). In the meantime, the name chouans was applied to all of them, giving general application to a nickname originally relating to bands of smugglers who imitated the call of the owl.
The arrival across the Loire of Vendéans heading for Granville after October 1793 changed the situation. The chouans rallied and joined in the battles before going back into hiding once the counter-revolutionaries had been repelled. But the arrival of the Vendéans upset the regional balance to the benefit of the chouans, who were freed from the pressure of the republican troops they had been fighting and which were redirected against the Vendéan column. Moreover, even though the Vendéans had been crushed, the republican armies emerged greatly weakened by a succession of battles. By the beginning of 1794 the republicans held the towns, main roads, and those parts of the countryside where the locals had stayed faithful to the Revolution. But several informal groups of chouans established themselves here and there along the coast of Brittany as far as the south of Caen, to the east of Le Mans and Angers. The leaders, mostly commoners identified by their peers and thereafter recognized for the leadership they had demonstrated in combat, had established fairly strong links. The factions that had developed within the revolutionaries and the exhaustion of their armies led to a certain stasis, confirmed by the peacemaking efforts of a few representatives on the spot, notably in Rennes. During the autumn of 1794, insurgents stopped being referred to as "bandits" and became once again "misguided brothers," who might be pardoned if they agreed to lay down their arms. The process, as in Charette's Vendée, ended with a peace treaty between the chouan general Cormatin and the Republic, signed at Mabilais, not far from Rennes, in April 1795. But, as in the Vendée, where the counter-revolutionaries had split over this point, some chouans, of whom the best known is Cadoudal, the powerful leader from the Morbihan, rejected any peace deal.
But peace did not last there either. It served only to allow preparations for fresh battles, with the chouans benefiting from direct aid from the English and from the gratitude of the émigré princes, thanks to Puisaye, who had gone to England. This support, which the Vendéans had lacked, benefited the chouans, but transformed the movement by placing it under the de facto control of the nobles wanting to conduct a war in France against the Revolution and who saw an opportunity to regain their power and prestige. The limitations of this new situation became obvious as early as July 1795, when the émigrés and soldiers who had landed from English ships in the bay of Quiberon were defeated, imprisoned, and shot by troops commanded by Hoche. Bad relations between the expedition leaders and the difficulty of commanding peasant armies unused to any form of military discipline led to a resounding defeat of the whole undertaking. While Brittany had mostly escaped the Republican ascendancy, the failure of the landing at Quiberon had catastrophic consequences. The radical counter-revolution seemed incapable of changing the balance between the armies. The comte d'Artois spent two months off the Ile d'Yeu before landing in France. His abnegation was not merely tactical: the Paris uprising was crushed, the royalist networks dismantled or weakened, and the strategy of the constitutional monarchists was henceforth to take power through the electoral process.
Thus between 1796 and the summer of 1797 a period of indecision over the fate of the armies ensued. Chouannerie, however dangerous, was not accorded the same priority as the Vendée. It needed only to be contained; it did not endanger the republican state, which had more to fear from enemies on its borders and the possible alliances of royalists in the southwest of the country. In Brittany and Normandy armed groups were crossing the countryside engaging in surprise attacks or individual assaults and were frequently assisted, notably in Normandy, by poor people driven by destitution. Young noblemen joined these groups, helped by links with England which had become entrenched via the Channel Islands. Facing them, republicans watched, organized, and repressed, sometimes barely within the limits of the law, as "counter-chouans" undertook what were real commando operations. A state of general insecurity reigned. Assassinations and the settling of old scores occurred, as well as executions of political opponents. The inhabitants were subjected to the passage of opposing troops and were themselves committed to one camp or the other. However, the local administrative framework was often respected, even if it was difficult to find municipal officials to appoint or to know whether some were covert royalists. Taxes were poorly collected and the presence of armed forces was indispensable, but extending the conflict to the rest of the country was unthinkable, and the moderate royalists who were competing with the republicans were not inclined to support the chouans and their noble leaders who wanted to return France to a bygone era (see the case-study in Bourgeon 1986).
After 1797, and the failure of the attempt by constitutional monarchists and conservative republicans to take power, the position of the radical counter-revolutionaries was strengthened. The chouans became a sort of shadow army, with a general staff in which nobles played a greater part, even if the established leaders, such as Cadoudal, remained in place. The chouan leaders, Bourmont, d'Andigné, Scépeaux, and Frotté, led henceforth an organized and hierarchical guerrilla war, with a more or less stable body of troops, depending on safe chateaux or forests, with arms and money from England. When needed, the nebulous chouannerie hidden within the peasantry could always be mobilized. The links with the émigrés, England, and the king thus give chouannerie its ideological importance, especially as networks of secret agents were criss-crossing France and preparing to retake the country by force of arms. The political aim of chouannerie is clear: the movement was participating in the counter-revolution in order to restore a monarchical, Catholic, and seigneurial state, in other words, essentially France as it was before 1787.
This militarization reached its peak in 1799, linked to the great offensive launched against the Republic by the coalition. On every front - Italian, Dutch, Swiss, German - armies were engaged in significant operations. In the west, war resumed after overt preparation by the chouan leaders, who rallied their troops and organized their offensive operations by placing whole regions under military control. The counter-revolutionary offensive was, however, brought up short; there was no similarity in outcome between different theaters of war and, while Italy had virtually rid itself of French republicans, the latter were fighting to the death in Switzerland, defeating the Anglo-Russians in the Netherlands and had scattered the thousands of men who had laid siege to Toulouse.
In October 1799, the chouans succeeded in seizing a few towns in the west (Le Mans, Saint-Brieuc, and Nantes) before falling back to their preferred territory. The armies that had been raised to the south of the Loire had not been victorious, confirming the military defeat of the Vendée. Bonaparte, as soon as he was made Consul, opened negotiations with the chouan leaders, granted freedom of worship, made contact with Stofflet's former secretary, the abbé Bernier, in order to prepare the Concordat, and tried to win over the chouan leaders, by force or persuasion. Cadoudal resisted but left France for the time being; Frotté was taken and shot as a general warning; and others fell into line sporadically. The glory days of chouannerie were at an end.