General Howard's command, after discovering signs of the Indians at the mouth of Crandall Creek on Clark's Fork on September 8, had, in fact, continued down the stream, where Sturgis's couriers to the miners found them. Howard quickly responded with a message telling Sturgis of the Nez Perces' presumed course (possibly even toward the Stinking Water) and urging cooperation. "If you can check them in front, I will be able to close on them and strike them from the rear." [29] (As previously stated, however, the couriers did not reach Sturgis.) In the rain and cold of Sunday evening, the ninth, one of Fisher's men killed a wounded Nez Perce discovered near the scout's camp. Another man scalped the dead tribesman, hiding the trophy from Howard's view when he approached to alert them of Sturgis's presence "within twenty miles" and that a fight seemed imminent the next day. Instead, on the tenth, Fisher's scouts found the Indians' trail bearing southeast through the foothills toward the Stinking Water and then detected their apparent stratagem in turning Sturgis in that direction. As Fisher explained:

The enemy followed the trail towards the Stinkingwater about two miles, and then attempted to elude pursuit by concealing their trail. To do this, the hostiles "milled," drove their ponies around in every direction, when, instead of going out of the basin in the direction they had been traveling and across an open plain, they turned short off to the north, passing along the steep side of the mountain through the timber for several miles. When we reached the point where the enemy had endeavored to cache their trail, we scattered out in every direction looking for it. At first the scouts were at a loss to know which way they had gone but after spending some time in the search I was so fortunate as to stumble onto the trail. I then went back to apprise the command of this new change of direction. [30]

Fisher and his men later trailed the Nez Perces through what Fisher described as "a very narrow and rocky canyon" leading down to Clark's Fork. While the Nez Perces' course to Clark's Fork is not known with certainty, several scenarios based upon longtime study of the terrain are possible. One possible route would have the Nez Perces milling their horses in a grassy swale a mile or two south of Dead Indian Pass, then moving first north and then northeastwardly down Bald Ridge, parts of which would have afforded some concealment from Sturgis's scouts. By this route, they could have reached the upper end of Newmeyer Creek and followed its slope eastward, then northward to reach Clark's Fork two miles below the mouth of Clark's Fork Canyon. Another course would have them mount Bald Ridge and move two miles southeast toward the Stinking Water before milling their animals in a swale, then move east-northeast via the head and main course of Paint Creek to reach Clark's Fork. Finally, a somewhat longer and less direct route would have the Nez Perces move south up Dead Indian Creek, surmount a divide leading to the upper drainages of Trail and Pat O'Hara creeks, mill their horses in a swale along the latter stream, and then follow it in swinging east and north, circling around the east flank of Pat O'Hara Mountain and through Oxyoke Canyon before heading north to Clark's Fork. These routes (not all of which have been completely evaluated) either contain, or are likely to contain, at least some topographical elements that might conform to Fisher's "narrow and rocky canyon" reference. Whichever route the tribesmen chose, however, it is certain from the military documents and reminiscences that Howard's command trailed them over the same course and that Sturgis's command eventually did likewise in its return to Clark's Fork. [31]

Howard followed with his men, disappointed that he was still at least one day behind the Nez Perces and that Sturgis had not stopped them. His command continued down the right bank of Clark's Fork and bivouacked about two miles below the canyon. During the day, the scouts found and buried the bodies of three prospectors killed by the warriors as they passed. "They will kill everybody who falls into their hands now," wrote Major Mason, "in order to prevent the news of their movements from being known to those in front." [32] On the eleventh, joined by a few Crows arrived from the agency, they found a wounded German who reported that his two partners had been killed by the Nez Perces on Crandall Creek. [33] "If we ever get these fellows," allowed Mason, "they must swing—unfortunately, catching comes before hanging." [34] Again, Howard tried to communicate with Sturgis, telling that officer that the Nez Perces were now in his (Howard's) front and admonishing him that they must be stopped before reaching the Yellowstone. "Let me know just where you are and what you are doing," he wrote. [35] That evening, when Howard's soldiers camped along Clark's Fork, Sturgis's men, having that day followed the trail from Sunlight Basin, saw their fires and camped only four miles behind them. At Sturgis's approach to the spot he had vacated the evening of the eighth, Howard, with Major Mason, rode back to assume overall command. The two conferred, and, reported Sturgis, "we entered into mutual explanations, and had the poor satisfaction of exchanging regrets over the untoward course which events had taken." [36] A witness commented on the meeting: "[Sturgis was] so bitterly chagrined at the escape of the Indians from one of the best laid traps of nature and man, that he exclaimed:'Poor as I am I would give $1,000 if I had not left this place.'" [37] On consultation, the two agreed that Sturgis should press on after the Nez Perces by forced marches, accompanied by Lieutenant Otis's two mule-mounted howitzers, Major Sanford and fifty cavalrymen under Captain Charles Bendire, and Lieutenant Fletcher's twenty-five scouts. Hopefully, this force could overhaul the tribesmen and strike "a telling blow" before they crossed the Yellowstone. Howard would follow with the balance of the command "as rapidly as possible." [38] They further agreed to send a dispatch to Colonel Miles at the Tongue River Cantonment, explaining how the Nez Perces had managed to get past them, their (Howard's and Sturgis's) intended movements, and the anticipated route of the caravan after crossing the Yellowstone River. In the missive, drafted September twelfth, Howard asked Miles "to make every effort in your power to prevent the escape of this hostile band [should Sturgis fail to halt them], and at least hold them in check until I can overtake them." [39]

At 5:00 a.m., Wednesday, September 12, Sturgis and his augmented force, "almost breakfastless" despite meager provisions that had arrived from Fort Ellis, proceeded down the river toward the Yellowstone through a mist that grew into a torrential rain. They were also impeded by the necessity of fording Clark's Fork numerous times. "We had nothing to eat," recalled one trooper, "so we merely drew our belts one hole tighter, took a drink of water, threw the saddles on our horses . . . and hit the trail." [40] Sturgis drove his force mostly at a trot, and by 1:00 p.m., at the first halt, they had covered thirty miles. At 4:00 p.m., the men passed an abandoned Nez Perce camping site, but Sturgis kept on for seven more hours before calling a halt for the night about eight miles above Clark's Fork's confluence with the Yellowstone. Trooper Theodore W. Goldin described the scene:

Some one discovered a fallen tree, and every one fell to bringing in arms full of brush, among which was some that was dry enough to kindle into flame. In a few moments that old tree was blazing merrily, and the outfit, officers and enlisted men alike, in wet, steaming overcoats, edged in as close to that roaring fire as they dared, seeking to thaw out the stiffness of their day's ride which we were told exceeded sixty miles. [41]

Most of the soldiers then succumbed to their weariness and "sank into a damp, restless, unrefreshing sleep." On directions of the officers, the packers set the mules to graze to stop their braying, fearful that the noise would warn any Indians nearby of the troops' presence. [42]

The Nez Perces, were, in fact, close at hand, having forded the Yellowstone on September 12 and moved downstream about six miles to camp. According to their own sources, a young man named Ilatakut (Bad Boy) had guided them in the circumvention of Sturgis and the evasion of Howard in the mountains and foothills. The large body of tribesmen, with all their horses and belongings, had beaten both officers to the Yellowstone, crossing below the mouth of Clark's Fork. [43] They at last recognized the futility of attempting a union with the Crows, whose tribal interest dictated their continued allegiance with the government, although it is likely that much sympathy of the Crows rested with their old friends in their plight. By now, the once-remote Canadian option loomed invitingly as the Nez Perce leaders cogitated over what to do and where to go, as it had increasingly since their sojourn in the national park.

On fording the Yellowstone, the tribesmen continued downstream to the grassy flats bordering Canyon Creek above its mouth, then turned up the creek bottom perhaps three miles where they encamped for the night, unaware that Sturgis was significantly gaining on them. Below Canyon Creek, the Yellowstone Valley narrows to less than one mile in width. The presence of the community of Coulson at that spot perhaps influenced the Nez Perce leaders to avoid an encounter with the settlers there by moving instead up Canyon Creek. [44] The lush Clark's Fork bottom of the Yellowstone Valley had only recently attracted settlers, and many had moved into the area in June.

Early the next morning, Thursday, September 13, a party of warriors started down the Yellowstone Valley to forage for supplies and encountered several newly established homes. Near the mouth of Canyon Creek, they alarmed settlers Elliott Rouse and H. H. Stone, who fled downstream to a neighboring ranch. The warriors stopped at the stage station built in the summer of 1877 on the east side of Canyon Creek and about one-half mile from the Yellowstone, and as the driver and passengers in an arriving coach—one a vaudeville entertainer named Fanny Clark bound for the mining camps—scurried into the brush, they fired the buildings and haystacks, scattered the mail, and tried to destroy a mowing machine. (While in hiding, Edwin Forrest, who ran the station, killed Miss Clark's little dog, which persisted in barking and drawing the Nez Perces' gunfire. He tried to slit the throat of his own somewhat larger dog, but the animal broke free of his grasp. "Nursing the cut kept the dog too busy to bark any more," wrote Scout John W. Redington. [45]) Reportedly, some warriors then mounted the coach and drove it over the prairie for amusement. Farther downstream, they found Bela B. Brockway's ranch and burned his hay house and corral. Again, most of the settlers found refuge in the bushes. But at the tract of thirty-year-old homesteader Joseph M. V. Cochran on the rich bottom five miles below Canyon Creek, two wolfers, Clinton Dills and Milton Summer, occupied a tent on the property when the Nez Perces arrived and killed both of them. Cochran himself was with some loggers upstream toward Canyon Creek when the warriors appeared. [46] Armed with a rifle, he approached and talked with them, and they eventually turned and rode off with his horses, but without harming Cochran. When he returned home, he found the bodies and that the Nez Perces had taken much property from his ranch, including clothing, utensils, tools, and ammunition. Some warriors ranged farther down the Yellowstone to the settlement of Coulson, near present Billings, where they burned a shack and exchanged shots with residents secured in hastily prepared rifle pits. They kept on to near the present town of Huntley before turning back to rejoin the main assemblage, then in process of moving up Canyon Creek. [47]