The fall of Huronia enabled the Iroquois to concentrate their subsequent war efforts on the French settlements in the St. Lawrence Valley. The French abandoned all their missions and positions west of Montreal, while to the south Fort Richelieu lay in ashes. As a result, all the major routes to Montreal - the Ottawa River, the Richelieu River and the upper St. Lawrence - were more or less under Iroquois control. The intensity of Iroquois incursions into French-held territory increased, and a virtually permanent guerilla war ensued. Unlike the colonists in New England and New Holland, the inhabitants of New France now had to endure war in the very heart of their settlements.
To meet the threat, there were only tiny garrisons and a "flying camp" of regular soldiers and volunteers. In 1651, it was decided to strengthen it by raising its numbers to 70. However, the next year it was disbanded for reasons of economy. It was revived in 1653 to assist the Trois-Rivières garrison, which was struggling to fend off Iroquois attacks, before being permanently disbanded. After 1652, the permanent garrison should have consisted of 15 soldiers in Quebec, 10 in Trois-Rivières and 10 in Montreal, with "another 14 soldiers in Trois-Rivières"; 
in actual fact, however, the garrison consisted of only 35 soldiers. Nevertheless, the French and Iroquois concluded a peace treaty in the fall of 1653, even though it was of short duration.
The establishment of the French mission of Sainte-Marie de Gannentaha in the heart of Iroquois country in July 1656 seems surprising at first. However, it was in response to the wishes expressed three years earlier by the Iroquois of the Onondaga nation. A party of soldiers led by Zacharie Dupuy accompanied the five Jesuit missionaries who founded this mission on the shores of Lake Gannentaha (now known as Lake Onondaga, southeast of Syracuse, New York). There were apparently about 20 soldiers in the party, recruited in France by Dupuy himself. 
The establishment of the Sainte-Marie mission did not please all the Amerindians however. The Mohawks were particularly opposed to this gesture of openness toward the French and mounted a few raids in the hope of breaking the peace. The number of ambushes increased considerably over a wide area in the fall of 1657. The situation of the French in the mission became untenable. They knew that, sooner or later, the Onondagas would once again rally to the other nations of the Iroquois Confederacy. To remain where they were was to accept a sentence of torture and death. Therefore, they secretly abandoned the camp under cover of darkness on March 20, 1658.