Van Rensselaer replied the next day but did not reprimand Smyth for not reporting in person, though he hoped "soon to have the pleasure of meeting you here." As for changing the plan of campaign, Van Rensselaer commented that, although he might be willing "as a citizen soldier, to surrender my opinion to a professional one," he refused to do so and patiently explained in some detail the reasons for his choice of Lewiston as a crossing point. The two senior officers in the Niagara were thus off to a bad start.

Two days later, Smyth reported that some of his regiments had arrived at Buffalo. They were half-trained recruits but Smyth intended to devote six hours to their drill, although he assured Van Rensselaer that "any orders I receive will be obeyed with alacrity." This proved to be somewhat short of the truth, however, as on October 5, when Van Rensselaer queried when he could expect him at a senior officers' conference at Fort Niagara, he received no reply from Smyth. On October 10, Van Rensselaer decided to cross the Niagara River and attack the village of Queenston on the Canadian bank. He ordered Smyth to march immediately to Lewiston with all the regular troops under his command. The attack, however, was canceled.

On October 12, Van Rensselaer informed Smyth that he intended to attack that night but Smyth was to keep his troops at Buffalo. Smyth replied that the state of the roads were bad and that his men had just received new clothing. They would, therefore, wash on the 13th but could march on the following day, although he warned Van Rensselaer his regulars were "but imperfectly disciplined or trained." He added that the British appeared to have gathered a large force opposite Black Rock and, since the 13th Infantry Regiment and the 2nd Artillery Regiment—both regular army units—had arrived at Lewiston, the time for Van Rensselaer's attack on Queenston was favorable and “may you conquer is my prayer." This was hardly an enthusiastic response. In any case, Van Rensselaer's attack across the Niagara on October 13 was a total defeat that resulted in the loss of about 1,000 Americans killed, wounded or taken prisoner. Eleven days after the battle, Van Rensselaer resigned his command and left for his estate on the Hudson River.

Smyth, however, faced very real problems. His troops, both regular and militia, were untrained, poorly clothed, unpaid, living in tents with winter coming and suffering from illness. As for maintaining "harmony and good understanding" among his units, the militia and volunteers proved almost impossible to discipline and desertion was common. Still worse, a unit of volunteers, who were ardent Republicans, tried to burn down a tavern in Buffalo owned by a Federalist. Smyth had to call out regular troops and artillery to quell the disturbance and to post a garrison of regulars in the village to maintain order. Among the worst of his problems was a shortage of provisions and Smyth blamed this on New York Brigadier General Peter B. Porter, a prominent local entrepreneur, who had been appointed the deputy quartermaster general. Relations between the two men became cool.

Comparing such paragons to the actual, miserable state of his regular troops was certainly taking liberties. Having got warmed up, a week later Smyth issued a bulletin to "To the Army of the Center," as he called his command, with even riper language: "Soldiers you are amply provided for war. You are superior in number to the enemy. Your personal strength and activity are greater" and "your weapons are longer." In contrast, the "regular soldiers of the enemy are generally old men, whose years have been spent in the sickly climate of the West Indies…. Come on my heroes." In a time when orotund language was common in public life, Smyth's bombast stood out and earned him some unflattering nicknames: "Alexander the Great," "Napoleon the Second” and—most cruel of all—“Van Bladder."

On November 20, 1812, Smyth terminated the truce with the British. This resulted almost immediately in an exchange of artillery fire at either end of the Niagara River. Fort Niagara traded rounds with Fort George in Canada while, at the southern end of the river, British artillery bombarded Black Rock, putting round shot through the house of Brigadier General Peter B. Porter. By November 27, Smyth was ready and issued his orders to his troops—they were to move at dawn the following day to their embarkation point behind Squaw (now Unity) Island. He added the embellishment: "Ye who have 'the will to do, the heart to dare,' the moment you have wished for has arrived. ...... Be strong! be brave! and let the ruffian power of the British king cease on this continent."

During the early hours of November 28, 1812, Smyth had ordered a number of detachments to cross the river and secure certain British batteries and bridges. These parties met with mixed success—one was cut off on the Canadian bank, the others returned without landing. Riding to the embarkation site, Smyth first heard news of the successful landing and, according to Dr. Cyrenius Chapin who accompanied him, rejoiced: "Huzza! Canada is ours! This will be a glorious day for the United States!" Unfortunately, when he learned a few minutes later that one of the detachments had been forced to surrender, his mood changed and "irresolution marked his countenance for the rest of the day."

It was a rotten day for the troops under his command. About 3,500 men assembled but the embarkation was confused and not completed until about mid-day. While the men huddled in the boats the artillery of both sides exchanged fire. Smyth was nowhere to be seen and there was much dissatisfaction in the ranks. In the early afternoon, the general decided to try what might be termed a military "Hail Mary" play—he sent an officer over the Niagara under a flag of truce to the British commandant at Ft. Erie with the suggestion that he surrender the fort "to spare the effusion of blood." The British officer, Lieutenant-Colonel Cecil Bisshopp of His Majesty's 1st Regiment of Foot Guards, who had been appointed inspecting field officer of the Canadian militia, immediately sent back a reply—probably as soon as he stopped laughing—that, if Smyth wanted the fort, he should be prepared to "fight for it." On receiving this blunt response, the general called a council of his senior regular officers who, after discussion, advised him to call off the operation. In the late afternoon, the troops, who had spent much of the day suffering under intermittent showers or rain, were ordered to "disembark and dine".

On December 12, the two aggrieved parties and their seconds rowed over to Grand Island and, against military regulations and New York State law, fired their pistols at each other. The island was probably chosen because its possession at this time was disputed between the United States and Britain and, since it was not legally part of the United States, specifically New York, a duel fought on it would not contravene any regulations or law. As it happened, both men missed their targets and, honor satisfied, "the hand of reconciliation was then offered and received." Thus mollified, the two generals returned to the mainland where, legend has it, they dined that night at a local tavern in a spirit of conviviality. 

It was clear, however, that Smyth could no longer remain in command, and his request for leave was swiftly granted by Dearborn and Eustis. He left Buffalo on December 21 and traveled to Virginia on a 75-day furlough. There was many a dry eye along the Niagara the day Alexander Smyth rode away—the feelings of the locals are clearly expressed in the words of one resident who remarked that the frontier had suffered enough from the "odious conduct of a demi-brute or whimsical savage who ought to be placed in a museum or sent into the forest with the orang-outang."

Smyth was gone but he was determined not to be forgotten. He and Porter continued their quarrels in print and, in the next several months, long letters written by the two duelists or their supporters appeared in the newspapers. This should come as no surprise as both men were lawyers and politicians—two occupations known for long-winded oratory. Smyth also tried to justify his conduct to the secretary of war, arguing he felt "keenly" that an effort had been "made to deprive him of any opportunity of vindicating his honor." He requested that a court of inquiry be held to investigate his command on the Niagara. "Although I have devoted myself to the service of the United States," Smyth complained "and all my official acts have proceeded from an ardent wish to serve them effectively, yet not having succeeded," he did not wish to appear for an inquiry in Washington "until I can deserve that applause of my superiors."  

In January 1813, William Eustis was replaced as secretary of war by John Armstrong, a much different man. Energetic and decisive, Armstrong decided to rid himself of the problematic Virginian and he hit upon a novel method. When new regulations were issued for the organization of the staff in March 1813, the office of inspector-general had disappeared and Alexander Smyth's name was no longer on the list of general officers. In effect, Armstrong had "legislated" Smyth out of the service, thus saving himself the time and trouble of holding an inquiry or possibly a court martial about his conduct.

Not unnaturally, Smyth was puzzled over his status and wrote Armstrong, requesting him to clarify whether "I am considered an officer of the army of the United States, or not." Armstrong does not seem to have replied to this request nor does he seem to have had any further correspondence with Smyth.

The last chapter in this curious tale of one of the early republic's most curious generals came in December 1813, when Smyth sent a petition to Congress. Stating that he had "not done or omitted any thing to the injury of the nation," to prove that that "affirmation is true, he believes he can satisfy a committee or committees of your honorable body, on short notice." Smyth being Smyth, however, he just could not resist a melodramatic flourish. It was impossible, he wrote, for him to return to civil pursuits "while the din of war continues," and he therefore desired "to serve, to die, if heaven wills it, in the defense of his country."