While all of this was occurring, Sturgis's command had descended Clark's Fork and crossed the stream to a plateau lying between it and the Yellowstone. Turning north, the soldiers located a ford (near where the present bridge crosses into Laurel) and, at about 10:00 a.m., began swimming their horses across the Yellowstone. Sanford's and Bendire's cavalrymen, along with Lieutenant Otis and the artillery, had dropped far behind because of their fatigued animals. Sturgis, in fact, seemed ready to halt his weary men, possibly intending to give up the chase altogether after gaining the north bank. While his scouts continued on the Nez Perces' trail, he penned a note to Miles, enclosing Howard's dispatch that had arrived, and sent it in duplicate via couriers down the Yellowstone to Tongue River.

The country entered upon by the Nez Perces and Sturgis on the north (west) side of the Yellowstone River was strikingly different from that they had known over previous days in the vicinity of the national park. The Yellowstone's left bank retreated in rolling fashion to form a lofty, broken scape of yellow clay ridges and plateaus, succeeded beyond by more, a tableland interspersed with broad valleys and sandstone buttes carved and weathered by millions of years of erosional action. Canyon Creek, on which the Nez Perces had camped the night of September 12, was dry in September except for infrequent alkali pools and represented more of a deep-walled slash through the grassy terrain. From the highlands bench overlooking Yellowstone Valley, the bed snaked its way south and east twelve miles down to the canyon mouth. Inside the canyon proper, a north fork fed into Canyon Creek. From the mouth, dominated by towering yellow, red, and gray-hued walls up to four hundred feet high, Canyon Creek ran southeast, entering the northeasterly flowing Yellowstone some six miles downstream from the place that Sturgis's troops forded. On either side, the bottom spread through a broad, mostly treeless, valley, or cove, through which rare tributaries fingered their way to the creek.

As the balance of Sturgis's troops waited on the left bank of the Yellowstone for the pack mules and rear guard to come over, a Crow scout rode up to announce that the Nez Perces lay just below and were headed toward the troops. [48] This news startled Sturgis. Peering downstream, Scout Fisher and his men could see a plume of smoke rising from buildings and haystacks ignited by the warriors miles away on the Yellowstone bottom. [49] Soon one of Sturgis's white scouts appeared with news that the main village was "going in a northwesterly direction" up Canyon Creek six miles away. The trumpeters sounded "To Horse," and the command set out at a trot. Two miles downstream, the troops received word from the scouts that the Nez Perces were headed toward the canyon of Canyon Creek, approximately ten miles north of the river. [50] At this, Sturgis veered his men north, away from the Yellowstone and toward the bluffs rising sharply four miles north to try and head off the tribesmen somewhere along Canyon Creek. Major Lewis Merrill's battalion of Companies F, I, and L (Bell, Nowlan, and Wilkinson)150 men strong—led the advance as the troops rode ahead with Company L in the lead. Wilkinson deployed his unit in line and advanced behind the scouts, while Companies F and I followed in columns of fours at his flanks. Captain Benteen's battalion—minus Company H, which served as rearguard for the command, but with Sturgis in attendance—followed in reserve. [51]

As Merrill's battalion advanced, in Wilkinson's front a long ridge rose up to three hundred feet above the surrounding ground and ran roughly southwest to northeast toward Canyon Creek. Its top constituted a broad plateau of up to one mile in width, and from this point, probably before noon, warrior marksmen first fired on Wilkinson's soldiers as they attempted to skirt the ridge and head off the main body of Nez Perces. The shooting brought the troops to a halt; they then began moving forward in mounted skirmish formation and started up the slopes of the ridge, firing their Springfields as they went, while Merrill's other companies under Captains Bell and Nowlan, strung out behind because of their worn-out animals, closed in and similarly disposed themselves. Gaining rising ground, the command could see the Nez Perce column bearing up the north side of Canyon Creek, the tribesmen and their camp dunnage moving along and the pony herd stretched out for a mile, all bound diagonally northwest, apparently headed for the mouth of the canyon that could not yet be discerned by the soldiers. As the troops trotted up the ridge (which Merrill at first mistakenly believed was the south side of the canyon), the warriors retreated, now bracing themselves behind the northwest edge of the plateau to deliver a rapid fire but ultimately withdrawing in the direction of the continually moving caravan. The army scouts, meanwhile, found themselves in front of the troops who were ascending the plateau and momentarily got caught in a crossfire—"a hot place," said Fisher. On top, the soldiers dismounted with Company F on the right and quickly stepped across the broad tract, finally settling at its northwest edge and continuing their desultory shooting at the warriors, who returned a brisk fire from the ravines and washes punctuating the broken ground that stretched to the canyon two miles distant. Fisher complained that the cavalrymen, "instead of charging which should have been done, dismounted about five hundred yards from the enemy's lines, deploying to the right and left, and opened a very rapid fire." [52] On the other hand, Merrill explained that "the men were almost entirely recruits, but dismounted and formed under fire, and moved rapidly to the front, driving the Indians with perfect steadiness and unexpected coolness and absence of confusion." [53] With the plateau cleared and in Sturgis's control, the troops finally beheld the panorama before them. Wrote Merrill:

The farther edge of the plateau being taken, it was then discovered that this was not the flank of the cañon, which could now be seen, with a broad valley some three miles wide intervening, amply intersected by ravines and gulches, in which the Indians were taking shelter to dispute further progress toward the cañon mouth. [54]

In fact, the "flank of the cañon," southwest of its entrance and forming its south side, was an imposing sparsely wooded four-hundred-foot yellow-walled butte (today called Calamity Jane Horse Cache Butte) that ran back nearly one mile from the mouth, while the opposite wall consisted of abruptly rising palisaded rimrock towering four hundred feet above the creek bottom. The half-mile-wide mouth, or gorge, lying between thus assumed both tactical and strategic importance, for through it the people needed to pass if they hoped to get away from the soldiers and protect their families and stock; they also needed the route in order to gain the open plains leading north. By blocking the canyon, Sturgis's soldiers could prevent the Nez Perces' entrance and likely end the conflict.

After nearly thirty minutes of largely ineffective firing from the brim of the plateau, Merrill's dismounted skirmishers pressed down its slopes and proceeded through the sage-and-greasewood-covered flat, pushing the warriors back toward Canyon Creek and the Nez Perce column, still in motion toward the canyon's mouth. A cold, fiercely blowing wind seems to have affected the shooting ability on both sides, and the soldiers, at least, had trouble gauging the distance and accordingly adjusting their sights because their bullets, when striking the damp ground near the warriors, kicked up but little dust. Fisher observed that the warriors stationed themselves between the soldiers and their own horse herd. They "fought entirely on horse-back, firing mostly from their animals and at long range, doing but little harm." [55]

"Fight at Cañon Creek, Sturgis. Sep. 13th." Lieutenant Fletcher's drawing affords a compressed (and thus distorted) view of the action, showing the positions of troops engaged on the ridges in the foreground and the Indians' withdrawal into the mouth of the canyon. Inset drawing in Fletcher, "Department of Columbia Map"

On gaining the plateau behind Merrill, Sturgis immediately comprehended the situation before him. His primary objective became the Nez Perce pony herd driven by the noncombatant women and children; he knew that to corral those animals would effectively stymie the people's advance. With the ground to his front torn up with ravines and ditches, Sturgis sent Captain Benteen, who with his battalion (reduced to Companies G and M) had assumed position on Merrill's left on the plateau, to ride to the west, skirting around the ravines and reaching negotiable ground near the base of the hills on the left, two miles away in a direct line, but about double that distance by traveling behind the plateau occupied by Merrill and then turning northeast toward Horse Cache Butte. [56] Benteen had earlier dispatched a platoon of Company M under Lieutenant Gresham to the western foothills, and he followed with the rest of his men. (Benteen's route on turning north probably approximated the course of the present Buffalo Trail Road north of Laurel.) On reaching the level plain beneath the west hills, Benteen was to charge his horsemen diagonally northeast, across the front of Merrill's troopers and across Canyon Creek, cutting off at least part of the horse herd before it entered the mouth of the canyon.