On September 11, 1775, the Americans were encamped south of Fort Saint-Jean. Their supply line consisted of a flotilla of small vessels operating on the Richelieu River. When a British schooner, the Royal Savage, threatened to disrupt this supply line, the Americans retreated to a more secure base on L'Île-aux-Noix.
On September 14, Schuyler learned that a force of Canadian Volunteers had taken the field under the command of James Livingston. Schuyler dispatched Major John Brown of Massachusetts to support Livingston with about 100 Americans and 34 Canadians. These men circled around Fort Saint-Jean and established a base between the American army and the friendly Canadians.
Meanwhile, hundreds of men had fallen ill in the American camp and were either discharged or sent south to recuperate. Fortunately, reinforcements started arriving at L’Île-aux-Noix, which partially offset the loss in strength. The new troops included a company of the 4th New York Regiment, 100 of Bedel’s Rangers, and 170 Green Mountain Boys.
Schuyler was also ill, and he soon turned over command of the army to Brigadier-General Richard Montgomery. Before he left, the two generals made plans for a new attack on Fort Saint-Jean.
The American plan was to divide into three parts: a) 500 men would circle around the fort, and cut the British supply lines, b) 200 men would establish a base south of the fort, and c) 350 men would defend the Americans’ own supply lines against the Royal Savage.
None of the American vessels was strong enough to confront the Royal Savage directly. Instead, the Schuyler and Montgomery planned on using the row galleys Hancock and Schuyler to fire on the vessel, while “picked men” aboard Liberty, Enterprise, and 10 bateaux would board it. 
American Invasion of Canada: September 16, 1775 (click to enlarge). The blue circles in the Richelieu River Valley show the positions of the main American army under Mongtomery at L'Île-aux-Noix, Brown's detachment near Fort Saint-Jean, and Livingston's Canadian forces near Chambly.
Schuyler left the army on September 16, and Montgomery led the attack against Saint-Jean on the following day. The operation faced minimal opposition. 
To the northwest, John Brown’s men captured eight wagons bringing supplies to the fort. Brown then threw down the bridge over Rivière Saint-Jean and erected a crude fortification from the wooden beams. Fort Saint-Jean was now in a state of siege, although the garrison did not know it.
To the south, the American flotilla advanced downstream and found that the Royal Savage was stationed near the fort and out of effective fire range. Hancock and Schuyler advanced a short ways further and fired on the fort and on British bateaux in the river. The British in Fort Saint-Jean replied with howitzer shells, but made no other movement.
Montgomery’s land forces disembarked without incident and reoccupied the abandoned breastworks south of the fort. In the words of Lieutenant John Fassett of the Green Mountain Boys, “We arrived at the breast work before night and found no Molestation, tho’ we expected a battle as much as we expected to get there. The whole army soon came up where we all staid that night and had nothing to cover us but the heavens and it was very cold and they flung Bom[b]s among us [i.e., howitzer shells] and we had a very tedious night of it indeed.”
1. Hancock and Schuyler each carried a double-fortified 12-pounder and 12 swivel guns. Enterprise was armed with two 6-pounders, four 3-pounders, and 11 swivel guns. Liberty was armed with two 2-pounders and 10 swivel guns.
2. The British commander, Major Charles Preston, had been abandoned by most of his Indian allies over the past week. Without these men, it was difficult to track (much less stop) American movements in the wilderness surrounding the fort. The Indians left for several reasons, including earlier diplomatic efforts by the Americans and the fact that their Canadian neighbors generally favored the American cause.