From Prescott on the 29th of October, 1812, Tom wrote to his mother of his delight at being once more a regular "in that distinguished old corps the 49th." It was indeed a fine regiment. Brock had led it in North Holland and in 1801 it had been on board the fleet at Copenhagen with Hyde Parker and Nelson; it is now the Berkshire Regiment and the name "Queenston" where its commander, Brock, fell, is on its flag. Though a soldier not a sailor, Tom had now one gunboat and three armed batteaux under his command, and, when writing, he had just arrived at Prescott with the American prisoners taken in the gallant action at Queenston where Brock was killed. His tone is serious and tender. "When the war is over I trust in God we shall all have a happy meeting again at Murray Bay, perhaps never more to part during our stay in this world." It was now his plan that if he should outlive the war he would go to Edinburgh, find a wife and settle himself on his property without loss of time. A few days later, on November 15th, he writes from Kingston of a lively incident in which he has taken part. With six schooners and an armed tug, the Oneida, of 18 guns, all full of troops, the Americans had appeared before the place. At 4 o'clock on the morning of the 10th the adjutant of the 49th came into Tom's barrack room to arouse him with the news that the enemy was thought to be landing a force five or six miles above the town. "He lit my candle," says Tom, "and left. I immediately jumped out of bed, dressed myself in a devil of a hurry and sallied forth to the Barrack yard where I found three Companies of the 49th under arms, Gunners preparing matches and artillery horses scampering out of the yards with field pieces." He was soon sent to hold a bridge about three miles west of the town. The ships kept up a fierce cannonade for some time but it was so briskly returned that in the end they drew away having lost four men. But they had command of the lake, a supremacy not to be challenged until a British Commodore, Sir James Yeo, arrived in the following summer.

In his letters at this time Nairne speaks of his heavy expenses and says that even if the opportunity came to visit Murray Bay he could not go for lack of money. So he begs his mother to build all the mills and houses she can, and thus to make the profits which he sorely needs. He complains of hearing from home so rarely: "You have only wrote once, I believe, since I came to the Upper Country. What in the name of wonder are you all about? I hope Yankey Doodle has not run off with you. I am sure there can be no complaints of my being negligent in this way."

The scene changed rapidly. Early in February, 1813, Nairne was sent to Niagara. Here for a time he was stationed at Fort George. The Americans were now menacing Fort Erie on the Canadian side of the Niagara River. But things were looking well for the British. On January 22nd the British Colonel Procter defeated the American General Winchester at Frenchtown near Detroit and made him and 500 of his men prisoners. Now young Nairne talked even of "extirpating" General Harrison whom the English were attacking in what is now the state of Ohio. But again high hopes were dashed. General Harrison succeeded in forcing the British to evacuate Detroit; then he invaded Canada, and before the campaign of 1813 was over he defeated the British badly at the river Thames in what is now Western Ontario. Meanwhile about Niagara there was some lively campaigning. In March Nairne describes an exciting night journey in sleighs from Fort George to Chippewa near Niagara Falls where an American landing was feared. Echoes of more distant wars reach this remote frontier. This was the winter of Napoleon's terrible retreat from Moscow and word comes, "glorious news certainly if true," that 140,000 French have been captured by the Russians.

Nearer home the chronicle was less glorious. The American fleet appeared before York (Toronto), burned the Parliament Buildings and public records, and carried off even the church plate, and the books from the library, of Upper Canada's capital, acts avenged by the burning of Washington later in the war. Flushed with success, the Americans now prepared to attack Fort George in overwhelming force. The 49th, Nairne's regiment, were the chief defenders. The attack came on May 27th, 1813. There was sharp and bloody fighting. Greatly outnumbered, the British were beaten; so hastily did they evacuate the fort that Nairne and others lost their personal effects. He writes, somewhat ruefully, that he has now only the clothes on his back and his watch, a purse, a family ring, and some trinkets. But this had its compensations; now he could carry everything in a haversack and blanket. Even paper, pens and ink are hardly to be got; he is writing on the last bit of paper he is likely to have for some time.

For many weeks the young man took his share in this campaigning in the Niagara peninsula. The British headquarters were by this time at Burlington Heights at the head of Lake Ontario, half way between Fort George and York, the ruined capital. By June the British had turned on the foe with vigour. On June 6th they rather stumbled into victory at Stoney Creek, capturing two American Generals, Winder and Chandler. On June 7th a British squadron, under Sir James Yeo, appeared off Burlington Heights, bombarded the American camp on the shore at Forty Mile Creek and compelled a retreat towards Fort George. Soon the British were menacing the enemy in Fort George itself. Nairne's letters, watched for, we may be sure, at Murray Bay with breathless interest, recount the incidents of the campaign. At Beaver Dam, only a dozen miles or so from Fort George, Lieutenant Fitzgibbon of Nairne's regiment, the 49th, entrapped an advancing party of Americans and, by the clever use of 200 Indian allies, filled them with such dread of being surrounded and massacred by the savages that nearly 600 Americans surrendered to little more than one-third of their number. These same wild Indians in their war paint were enough, Nairne thought, "to frighten the Black Deil himsel'," and their proximity in the campaign is one of many causes for which he thanks Heaven that the plague of war is so far removed from Murray Bay; even if it lasted for years, it would still not reach that remote haven, he says. Meanwhile Murray Bay can help him. Two pairs of socks, one flannel and one linen shirt, have been the modest increases to his wardrobe since the hasty exit from Fort George many weeks before. He begs his sisters to make him some shirts and socks, but not many, since on the marches, usually made at night, he has to carry all his belongings on his own back. The charge of a too elaborate transport service sometimes brought against the British army in modern campaigns seems to have no place in the War of 1812. The British, few in number and defending an immense area, had to do killing work. Nairne says that his men were able only rarely even to take off their accoutrements.

With the arrival of Yeo's squadron the war was again half military, half naval. Yeo was a brilliant young officer and the remote waters of Lake Ontario witnessed some clever naval tactics. The small fleets were evenly matched. Chauncey, the American commander, was very cautious and would not fight unless he could get the advantage of his longer range of guns, while Yeo, if he fought at all, preferred to fight at close quarters; so they manœuvred for position, each declaring that the other could not be brought to bay. On August 3rd, 1813, Nairne wrote from Burlington Heights to Malcolm Fraser. In an earlier letter that veteran had expressed the desire of dancing at Tom's wedding and Tom had told him, with the prophetic saving clause "should I outlive this war," that to see his friend of eighty years dancing would be a considerable inducement to marry. He hopes that they may soon discuss the war "over a good bottle of your Madeira at Mount Murray."

He calls Burlington Heights the stronghold of Upper Canada. "The situation we have chosen is by nature a strong position being bounded on the east by Burlington bay, on the south by a commanding battery, ditch and parapet, this being the only side bounded by the mainland; on the west by a morass and creek; on the north by the continuation of this same creek, which here discharges itself into Burlington bay. The height of the land above the level of the water all round is upwards of 100 feet and the only side therefore necessary to fortify is the south, which I assure you is pretty strongly so." Here was the chief British supply depôt and Nairne had just been sent thither to aid in repelling a menace from the American fleet. He had brought his force from Ten Mile Creek, in boats, on the open lake, and the journey, lasting all day, was ticklish enough. All the time the American fleet was in pursuit and it reached the narrow gateway to Burlington Bay only an hour and a half after Captain Nairne entered. The enemy intended to storm the heights, and landed 800 men for that purpose; but finding the position too strong, they re-embarked their force at daylight on August 1st, and bore away for York (Toronto) where they wrought new havoc in that undefended and "much to be pitied town."

On August 20th Nairne writes, still from Burlington Heights. This, his last letter, gives a dramatic account of a running fight between the rival fleets, in the dark, illuminated, however, by the flashes from their cannon:

It was a moment of great anxiety with us when the two fleets lay in sight of each other, the one wishing to avoid coming to hard knocks and the other straining every nerve to be at it. I rode 20 miles to see the hostile squadrons, and, for nearly two days, had the pleasure of observing their movements from the mountain at Forty Mile Creek, and I must confess I never saw a more gratifying or more interesting sight. At 11 o'clock on the night of the last day that I was there (the 10th inst.) Sir James Yeo contrived to bring them [the Americans] to a partial engagement and for an hour and a half the Lake opposite the Leo appeared to be in a continual blaze. I remained in a state of uncertainty as to the result till daylight when I observed the Yanky fleet steering for Fort George with two Schooners less than they had the evening before, and our fleet steering towards York with two additional sail. [They were the Julia and the Growler.] The Americans have besides lost two of their largest Schooners, which upset from carrying a press of sail, when our fleet was in chase of them.

While this dramatic fighting is going on before his eyes Nairne's one regret is that his present quarters are "completely out of the way of broken heads."