When Thompson returned to York factory in the spring of 1791, it was to find that great changes had taken place at the fort. Five years before, the tyrannous sway of old Humphrey Marten had come to an end, and he had been succeeded as governor by Joseph Colen. This man was to direct Thompson's movements during the next six years.

The new governor was a man of unquestioned ability; but his jealous and suspicious temperament made him work at cross purposes with the governor of Churchill, and brought him into frequent conflict with Tomison at Cumberland House. He had never caught the spirit of the aggressive policy initiated by Samuel Hearne, and preferred to develop the fur trade with the Indians who came down to the coast for trade, rather than to follow them to their hunting grounds. In his reports to the directors in London, he endeavoured to excuse his lack of enterprise by hurling vague accusations at his colleagues; while his subordinates, men like Thompson and Malcolm Ross, were irritated and provoked by the lack of support from headquarters which constantly frustrated their efforts to push forward the work of exploring the more remote interior.

The seven years of David's apprenticeship were now at an end, and he was engaged at a good salary as trader and surveyor to the Company. He was not yet, however, given an opportunity of practising his profession. The previous spring, an ice-jam at the mouth of the Hayes river had caused the water to rise, flooding the low land on which the factory was situated; and for a year or more, Thompson had to assist Colen in moving the fort to its present site on a high clay bank about a quarter mile further up stream.

Meanwhile Philip Turnor had returned from a journey to Lake Athabaska, and the report of his explorations had reached the directors in London. Proceeding from Cumberland House, he had worked his way north through Amisk and Pelican lakes to Frog Portage, a distance of one hundred miles. After crossing the portage, he found himself in the basin of the upper Churchill river. This stream he ascended as far as Isle à la Crosse, and thence he made his way through Buffalo lake and Lake la Roche to the Methy Portage. This portage marks the divide between the waters that flow eastward to Hudson Bay and those that discharge through the Mackenzie into the Arctic ocean. Crossing the portage, he descended the Clearwater river to its junction with the Athabaska, whose broad stream soon carried him to the lake of that name. This was the regular route followed by the Indians of the far north in their journeys to Hudson Bay.

Turnor's report filled the directors with a desire to dispute the trade of Lake Athabaska with the men of the North West Company; and they bombarded Colen with instructions to send Ross and Thompson to that region. But to Colen's mind there was a more pressing necessity nearer home. The North-Westers had entered the rocky belt to the south-west of York, and had monopolized trade throughout the irregular series of lakes and rivers which form the tributaries of the Nelson and lower Churchill, thus challenging the "English" on their home front itself. Accordingly Colen ignored the instructions from London, and despatched Ross and Thompson into this "muskrat country," as it was called, with orders to build posts at strategic points and restore the trade of the Company.

On the 5th of September, 1792, Thompson set forth with two canoes on his first independent command. Rounding the point from York factory, the canoes swung into the broad channel of the Nelson river. By the end of the month they were well above Split lake, Thompson making a survey as they moved along. At this point one of the canoes turned aside to ascend Grass river, while Thompson with the other continued along the main stream until he reached the upper end of Sipiwisk lake. Here in a little cove formed by two projecting points of rock, with the dark spruce forest at his back and a view to the south west over the island-studded lake, he built his first trading post, and settled down to face the winter in a country almost devoid of fish and game.

His heart, however, was set on exploration. From the Indians he learned that, besides the well-known route which had been followed by Turnor to Lake Athabaska, there existed another, north from the Churchill river to Reindeer lake, and thence westward by way of the Black river to the east end of Lake Athabaska. This route he made up his mind to explore.

Accordingly, when the ice had cleared from the rivers, he set forth alone without any help or encouragement from headquarters. Descending to the lower end of Sipiwisk lake, he turned to the left and passed by a series of portages through Wintering, Red Paint and Burntwood lakes to the Missinippi or Churchill river, up which he paddled for a distance of thirty-three miles. But the Indian guides whom he had expected to meet failed to put in an appearance, and he was forced to turn back. He therefore descended through Burntwood lake and the Nelson river to York factory.

Colen had given the English directors to understand that he planned to send Ross and Thompson to the Athabaska country; and with the arrival of the annual ship in the autumn of '93, they wrote that they expected much good to follow from the projected expedition, and that they wished William Cook, who had accompanied David into the Muskrat country the previous autumn, to join with the others in the invasion of the far north. But Cook was not recalled from his post on Split lake, and Ross and Thompson were sent up the Saskatchewan to Cumberland House. Thence Thompson was despatched, not to Lake Athabaska, as he had expected, but westward along the river to a new post called Buckingham House, from which he rode still further west to the Beaver hills near the future site of Fort Augustus (Edmonton). Returning, he surveyed the Saskatchewan east from Buckingham House to the Forks, and from the Forks he resurveyed the rest of the river. From Cumberland House, he explored a new route through Goose, Reed, and Burntwood lakes to the Nelson, and thus opened up a direct line of communication between the dépôt at Cumberland House and York factory, much superior to the old course by way of Lake Winnipeg and the Hayes river.

Thompson's reappearance at York without having been to the Athabaska country made it necessary for Colen to do no little explaining to the impatient London directors. In a long letter to them, he hinted that it was Tomison who was responsible for the fiasco. Tomison, he said, had refused to pass his word for the advance of wages promised by the Council to those who would volunteer to accompany the expedition. Ross, he declared, was utterly disgusted with the repeated disappointments, and would have returned at once to England, had not Thompson prevailed upon him to make one last trial, this time by way of Reindeer lake. Thompson and Ross, he added, were being fitted out with canoes and supplies at York, and would be sent up the Nelson river track. The directors were deceived, and swallowed their disappointment, hoping to hear that the difficulties which stood in the way of the Athabaska expedition had been successfully overcome.

But, even now, Thompson was sent, not to the North, but back once more to the Muskrat country, this time to Reed lake. Here, in a district comparatively rich in fish, game, and furs, he built a house, and spent one of the coldest winters in the history of the Hudson Bay. While hunting and trading, he also prepared for the directors of the Company, the maps and surveys of the country which he had already traversed. In July of the following year, 1795, he paddled down the river on what was to be his last visit to York.

On this occasion Colen was absent on a trip to England, but the factory was seething with discontent. Thompson found the staff impatiently waiting, in order that he, the youngest and bravest among them, might take the lead in drawing up a statement of the grievances which they suffered under Colen's rule. This office he accepted, although with some hesitation on account of the absence of the governor. Assisted by his friend the surgeon, he drew up a statement which Colen declared seriously prejudiced him in the eyes of the directors; although, according to Thompson, not one half of the evils were even mentioned of which the staff had cause to complain. Thompson was not ashamed of the part he had played in this mutinous outbreak. As soon as he had left the service, he took the opportunity of explaining to his old chief that he was the author of the protest which had so much displeased him. "Many of us," his letter concluded, "acknowledge with readiness that you have some good qualities, and I once had the greatest respect for you; I have some yet, but——it is not my wish to say those things which I know you do not wish to hear. How is it, Sir, that everyone who has once wished you well should turn to be indifferent to you, and even some to hate you, although they are constant in their other friendships?—there must be a defect somewhere. The fact is, that from your peculiar manner of conduct, you are also one of those unfortunate men who will have many an acquaintance, but never a real friend."

Thompson's final break with Colen did not, however, occur until two years later. He turned in his furs, and without waiting, except to secure supplies for the coming winter, went back to his duties in the Muskrat country. This time he built a house far to the north on Duck Portage, the link connecting Burntwood lake with the Churchill river. When spring opened, instead of returning to York, he made ready for his dash to Lake Athabaska.

Formal permission had reached him from Colen, sanctioning his venture into the unknown wilds. This, however, meant nothing, because it was not accompanied by help of any kind. At that moment, indeed, the Company was seriously crippled for lack of men to keep up the few inland trading posts that then existed, for the war which was raging between England and France had drained the Orkney islands of all men who were fit for service in the army and navy. The few miserable dwarfs who could be obtained for the fur trade excited the contempt of even the Indians.

Thompson, nevertheless, was not to be deterred from his enterprise. He proceeded at once to Fairford House, the trading post kept by Malcolm Ross on the Churchill near the mouth of the Reindeer river, where he hoped to get some assistance. To his great disappointment, he found that not a man could be spared from the trade in furs. There were, however, a few Chepawyan Indians lingering about the fort and from among these he managed to engage two young men. Kozdaw and "Paddy" had hunted for two winters in the country he was about to explore, although neither of them had ever been on the rivers and lakes in summer. Their only practice in canoes had been to lie offshore in the lakes on a calm day, watching for the deer to take refuge from the flies, and this gave them no experience of the currents and rapids of rivers; yet, such as they were, Thompson had no choice but to take them.

The first task was to construct a canoe. Having searched the forest for a supply of birch bark, they made a boat seventeen feet in length. Into this they packed their meagre outfit, a fowling piece with forty balls, five pounds of shot, three flints and five pounds of powder, a fishing net, a hatchet and a small tent of grey cotton. These articles, together with a few handfuls of beads, rings, and awls for trading, made up their terribly inadequate equipment.

In the grey dawn of a June morning, 1796, Thompson launched his canoe on the turbid waters of the Missinippi. The party advanced rapidly, making a survey as they went. For supplies they relied on their solitary net and gun. Turning into the Reindeer river, they worked their way north against a moderate current to Reindeer lake. A hundred miles up the west coast of this lake brought them to a point clothed with tolerably good pines. This point Thompson noted as a suitable site for building a trading post on his return.

The whole distance through which they had come had a barren, rocky appearance, relieved only by patches of stunted birch, aspen, and spruce. Since there was little or no soil, the trees stood with their roots interlaced like the trees on the frozen lands of Hudson Bay; and, like them, they were kept moist in summer by the wet moss with which their roots were covered. Through wide stretches the forest fires had passed, leaving the country unsightly and ghostlike, and destroying the wild animals of the forest. Thompson was now in fact approaching the northern limit of trees, beyond which stretch the barren lands, the home of the musk ox and caribou.

In order to avoid the wide circuit of the Cochrane river, which flows to Reindeer lake from Lake Wollaston, the guides directed Thompson up a stream that emptied from the west a few miles north of his point of pines. From the head of this stream there was a passage by a series of ponds and brooks to the south end of Wollaston lake. But the water was low, and they were forced to carry their packs for the better part of fifty miles, stumbling over the rocks and wading through the marshes, while clouds of mosquitoes buzzed about their defenceless heads. It was a welcome relief when they launched out on the clear and deep waters of Lake Wollaston, which they crossed without trouble to the Black river. Here they made camp on the evening of June 23, and rested while Thompson took observations and made up the notes of his survey.

Two days later they were once more under way. Lake Wollaston, as Thompson discovered, was situated on the height of land between the basins of Hudson Bay and the Mackenzie river. Part of its waters discharged eastward and south into Reindeer lake, while part flowed westward through the Black river into Lake Athabaska. From this curious circumstance, the lake was known to the Indians as "Lake Manito," and was considered to be of supernatural character. Entering the Black river, the party passed at first through the quiet reaches of the upper river, in a wretched country of solitude, where the wild laugh of the loon alone woke the echoes of the barren hills. Presently the banks closed in, and as the current stiffened, they had to paddle vigorously to avoid the projecting rocks. Finally an expansion of the stream brought them to Black lake. It was during this stretch that they came upon the only human beings they had so far encountered—five tents of Chepawyans, hunting and fishing in an otherwise deserted land.

They could afford but one day to enjoy the hospitality of the Indians. From Black lake, the river tumbles in two wild cascades to the level of Lake Athabaska. A series of rapids, cutting through a high hill, warned them that they were approaching the first of the falls. For half a mile they shot the rapids to a point where the river is compressed within a channel only twelve yards in width. At the end of this channel, the current rushed against a projecting ledge of rock with such force that the whole river seemed to be turned up from its bottom. The dashing of the water against the rocks, the deep roar of the torrent, the hollow sound of the fall, in the midst of the dark, high, and frowning hills, made a sight so grand and terrible that Kozdaw and Paddy were awe-struck, and offered their simple tributes to the manito of the fall—the one a bit of tobacco, the other a ring. Past this fall the travellers descended by a well-beaten native trail. A second series of rapids and a second fall brought them to the last lap of their journey, and they paddled quietly for six miles into the east end of Lake Athabaska. Here they passed the night, resting from their dangers, toils, and sufferings under a pine tree which had been lopped and marked by Philip Turnor in his survey of 1791.

Thompson's heart was thrilled by the thought that he had finally accomplished the journey on which for the last five years his heart had been set, and that in so doing he had blazed a trail through the wilderness over ground which the feet of white men had never trod before. He was sobered, however, by the prospect of the long and difficult journey home. His net and gun afforded but a scanty supply of food, and should these fail him, there was but slight hope of succour. But gloomy as were his forebodings, it was well that he did not know what lay before him.

Half way up the Black river, he encountered one of the rapids which was broken about the middle by a twelve-foot fall. Portaging past the fall, he attempted to "track" the canoe up the rest of the rapid. The two Indians were ashore tugging at the tow-line, while Thompson in the canoe tried to steer and at the same time direct their movements. Near the head of the rapid there was at the water's edge a tree which blocked their progress, and as the Indians stood hesitating which side of it they should pass, the canoe sheered off across the current. An upset was inevitable, had not Thompson waved to the Indians to let go the line and leave him to his fate. Springing to the bow, he cut the rope off short with the clasp knife which he kept in his waistcoat pocket, and got the head of the canoe around into the stream just in time to take the plunge over the cataract. For an instant, Thompson was buried beneath the boiling water at the foot of the fall. Striking his feet against the bottom, he pushed himself to the surface close to the upturned canoe. This he seized and dragged through shallow water to the beach. The Indians came rushing to his assistance, and, while he lay on the rocks, bruised, bleeding, and exhausted by his exertions, they searched the shore below the rapids for what could be recovered of their precious kit.

The gun, the axe, and the tent had remained fastened in the canoe. In half an hour's time, the Indians brought back the cork-lined box containing Thompson's instruments and the maps of his survey, together with their three paddles and a pewter basin. Not one moment was to be lost. Thompson's body was naked except for his shirt and a thin linen vest, and his companions were in like condition. The small tent they tore into three pieces with which to wrap themselves as a defence against flies by day and chill by night. Worse still, Thompson found as he painfully raised himself from the rocks that the flesh of his foot had been torn away by the impact of the jagged stones of the river bed, and a part of his share of the tent had to be taken to bind the wound.

The first duty was to repair the canoe, and the Indians were sent to the woods to procure gum from the pines. The question was then how to light a fire, for they had neither flint nor steel. Thompson pointed to his gun from which they took the flint, and with the steel blade of his pocket knife they struck a spark. When the gum was melted, they repaired the canoe and carried their kit above the fall and rapids. The Indians shouldered the canoe, while behind them the wounded leader hobbled painfully along under the burden of gun, axe, and sextant case.

Night had fallen before they found time to make a fire and warm themselves. Their situation was enough to strike terror into the boldest heart. Destitute, almost naked, and suffering from the weather, they faced a journey of three hundred miles through a barren country. Yet Thompson did not despair. For two days they paddled and portaged up the river without a bite to eat. On the afternoon of the second day they saw two gulls hovering over a reedy bay as if to protect their young. They found the nest and in it three young gulls, but the few ounces of meat which they were able to pick from their miserable carcases sufficed only to sharpen their hunger.

The next day as they went along, Thompson remembered an eagle's nest on the banks of a small lake before them. When they came to the lake they found the nest in the spreading branches of a birch tree, about sixteen feet above the ground. Kozdaw had barely time to climb to the nest before the old birds arrived. Paddy and Thompson, with shouts and stones, succeeded in preventing them from attacking Kozdaw, while the latter threw the two young eagles to the ground. The birds fought with beak and claw for their lives, but were finally killed and flung into the canoe.

In the evening, they opened the eagles by the gleam of the camp fire, and divided the meat and yellow fat into three equal portions. While Kozdaw roasted his meat and oiled his body with the fat, the others ate only the fat, reserving the meat for next day. In the night they were both awakened by a violent dysentery, which continued to plague them for many days, although a strong infusion of a certain dried moss, known as Labrador tea, brought them some relief.

Day by day they continued their voyage, subsisting on the wretched crow-berries of the far north. By the sixteenth of July, Thompson and Paddy were like skeletons, from hunger, dysentery, and cold. On that day Thompson scratched what he thought was his dying message on a scrap of birch bark which Kozdaw was to carry back with him to civilization. Late in the afternoon, as they paddled weakly and painfully along, they came upon two tents of Chepawyans. The savages pitied their condition and restored them with broth. From them Thompson procured some provisions, a flint and a few rounds of ammunition, together with a pair of shoes each for himself and his men. Thus they were able to proceed on their journey, and arrived without further adventure at Fairford House after an absence of thirty-one days.

At Fairford House Thompson was joined by Malcolm Ross with a stock of provisions for the northern trade, and together they returned to build a trading post on Reindeer lake. Along with the supplies, Ross brought a letter from Colen to Thompson, containing a curt order that he should cease his surveys and explorations. This was his reward.