Word of the attack on the Kamiah people decided Howard to forsake his original plan and to pursue the Nez Perces in a direct movement across the Bitterroot Mountains on the Lolo trail. Over the next few days, he formulated his plan while awaiting reinforcements. Essentially, he would proceed with three columns. The right column, personally commanded by Howard, would keep on the nontreaties' trail all the way to Missoula. It would consist of a battalion of Fourth Artillery under Captain Miller—Companies A, C, D, E, G, L, and M; a battalion of infantry under Captain Miles—Company H, Eighth Infantry, Company C, Twelfth Infantry (both arrived from Fort Yuma, Arizona Territory), and Companies C, D, E, H, and I, Twenty-first Infantry; and a battalion of First Cavalry under Major George B. Sanford—Companies B, C, I, and Kall cavalry companies not previously extensively involved in the campaign. This command of 47 officers, 540 enlisted men, 74 civilians and Indian scouts, and approximately 70 packers would depart Kamiah on Monday, July 30. The left column—designated to march through the Coeur d'Alene country over the Mullan Road to Missoula, where it would meet Howard—was, at Inspector Watkins's behest, to check potential allies of the Nez Perce fighters among disaffected area tribes while cooperating with Howard's principal force. This column, commanded by Colonel Wheaton, would comprise the ten companies of his Second Infantry, en route from Atlanta, Georgia, since July 13; Companies F and H, First Cavalry; and two companies of mounted volunteers from Washington Territory. Wheaton's command numbered 36 officers and 440 enlisted men. To protect the settlers on the Salmon and the Camas Prairie from further harassment, Howard would posture his reserve column under Major Green, First Cavalry, at Henry Croasdaile's ranch, a centralized location on Cottonwood Creek ten miles from Mount Idaho and sixteen from Kamiah. [27] This command comprised Companies D, E, G, and L, First Cavalry; and Companies B and F, Twelfth Infantry, besides a unit of Warm Springs Indian scouts. The force numbered 22 officers, 245 enlisted men, and 35 Indian scouts. Green would oversee an army subdepot at Kamiah with an artillery detachment and two pieces stationed there, while manning an outpost at Mount Idaho for the local volunteers. Green's command would make frequent patrols of the crossings of the Salmon River and the South Fork of the Clearwater, and the country between the Salmon and the Snake, with instructions to bring in any parties or families associated with the nontreaty Nez Perces. [28]

Colonel Wheaton and the Second Infantry reached the theater of operations on July 29, having traveled by rail to Oakland, California, by steamer to Portland, and by boat up the Columbia River to Lewiston. Howard returned to Kamiah on July 26, ready to spend the next three days crossing his enlarged command over the Clearwater in canvas boats preparatory to marching east on the Lolo trail. That same day, Companies (Batteries) C and L, Fourth Artillery, arrived from San Francisco to augment Miller's battalion with nearly fifty more men. Two days later, Howard accompanied McConville's men northeast to Weippe Prairie and returned without finding any Nez Perces. Following that scout, the Washington volunteers were discharged. Also on the twenty-eighth, Major Sanford with Companies C, I, and K, First Cavalry—the head of Green's column—arrived at Kamiah from Fort Boise, adding 140 more soldiers to Howard's army, along with 24 Bannock scouts, traditional enemies of the Nez Perces who were decked out in uniforms with bright sashes of stars and stripes. With the additions, Howard's force numbered some 730 officers and men. Also, a mule train of 350 beasts made ready to haul supplies for the army, while the artillery complement of two Gatling guns, two howitzers, and a small Coehorn mortar, all dismantled, would also be transported by mules. While the expedition assembled, Captain Jackson's company of cavalry patrolled as a picket guard a short distance up Lolo trail. On the evening of July 30, Sanford and the last soldiers crossed the Clearwater. Outfitted with twenty days' rations, General Howard's army ascended the Lolo trail on Monday, July 30, beneath a driving rainfall that "renders the mountainous trail slippery and exceedingly difficult." It had been two weeks since the Nez Perces departed for Montana Territory over the same route. [29]

In 1877, the Lolo trail stood as the major east-west linkage between the Bitterroot Valley in Montana Territory and north-central Idaho Territory. From the area of Kamiah, the trail ran approximately one hundred miles northeast, penetrating densely forested lands in traversing Idaho's Clearwater Mountains and Montana's Bitterroot range. A product of Pleistocene glaciation, the region was drained by the Bitterroot River on the east and the Lochsa and Selway rivers flowing west from the mountains to form the Middle Clearwater. The country—composed of myriad landforms of undulating ridges, swampy meadows, and peaks rising to seven thousand feet in elevation—in 1877 afforded a lush beauty complicated by an inaccessible character that made passage an arduous undertaking. Two primary features were the Lolo Pass (now called Packer's Meadows), a spacious, level hollow of about fifty-two hundred feet elevation at the divide between the Bitterroots and the Clearwater Mountains, and, a short distance below on the Montana side, the thermal waters known as Lolo Hot Springs, a traditional place for wayfarers to rest and relax. From there the trail paralleled Lolo Fork, an eastward flowing tributary of the Bitterroot River. The route had been used by Indians for generations preceding the arrival of white men in the region. Lewis and Clark followed portions of it in their passage to and from the Pacific Ocean in 1805 and 1806, and the trail—also known as "Lou Lou" or "Loo Loo"had assumed its present designation by the 1860s, when early topographers referenced it on their maps. Its passage was never easy, owing to its heavy timber growth and commensurately large proportion of uprooted trees felled by windstorms and heavy snows. Moreover, the trail alternately ascended and descended numerous mountains and saddles rather than following one long ridge, a wearing trek for those constrained to attempt it. In 1866, at the time of the Idaho and Montana gold rushes, a congressionally funded party—headed by Wellington Bird and Sewell Truax—surveyed and started building a wagon road on the Lolo trail, the ax men clearing many trees along the route and grading some of its steeper sections. It was along the line of the Bird-Truax improvements that the Nez Perces and Howard's soldiers traveled in 1877. [30]

While the army remained in the area of Kamiah awaiting supplies and reinforcements, the Nee-Me-Poo took advantage of the delay and, in effect, stole a march on Howard. They started for the Lolo trail on July 15, just as Howard moved to ford the Clearwater and head them off on the north side, a plan that failed. At Weippe, twenty miles from Kamiah, the leaders paused to council—the first of several meetings held over the course of the next several weeks to define what their objectives should be and what means they should adopt to attain them. According to Nee-Me-Poo testimony regarding the Weippe council, the leaders were divided about what to do. Some, including Joseph and Ollokot, wanted to follow the Lolo trail to the Bitterroot Valley, then pass south and return to the Salmon and Snake river country via the Elk City Road or Southern Nez Perce Trail and Nez Perce Pass (southwest of present Darby, Montana). White Bird advocated going into Canada, while others, notably Looking Glass, argued forcefully for gaining the buffalo plains, where they might join with their friends the Crows. In the end, the proponents of going to the plains prevailed; Joseph, White Bird, Toohoolhoolzote, the Palouse leader Hahtalekin (who had joined with sixteen warriors), and Husis Kute all proclaimed unity in the plan. Although each band maintained its element of independence as before, Looking Glass seems to have emerged from the conference as the recognized military leader; because of his seniority and experience, his opinions carried the most weight among all the people.

On the sixteenth, their animals packed and the great herd of ponies moving forward, the Nee-Me-Poo started out on the trail to Montana. They left scouts behind to watch the movements of the soldiers. It was these warriors who alerted the people about Major Mason's advance on the seventeenth, which resulted in the exchange near Weippe Prairie. Looking Glass later led the warriors in the attack on the Kamiah subagency and the running off of many of the reservation people's horses. All this time, the main Nee-Me-Poo column, consisting of the leaders and warriors and their families, including the very old and very young, the wounded and lame, besides some two thousand horses and hundreds of dogs all stretched out for several miles, kept moving farther away from the army and deeper into the recesses of the wooded and mountainous terrain. What might have appeared a logistical ordeal occurred with precision and dispatch, the tribesmen's mobility due to the culturally ingrained responsibility each family unit had in organizing, packing, and completing the daily transport of its property and members in harmony with other band and tribe members, plus their long experience in the rigors of mountain-plateau travel. [31]

When the Nee-Me-Poo reached Lolo Hot Springs, they paused at a traditional camping site nearby. [32] There they received information that some soldiers lay ahead on the trail watching for their arrival. Although the people had succeeded in leaving Howard's troops far behind, they seemingly were unprepared for finding more soldiers in their front. In a significant statement transcribed much later, Looking Glass responded to the information, stating in essence "that he did not want to fight either soldiers or citizens east of the Lolo because they were not the ones who had fought them in Idaho." These people, he believed, had nothing to do with their problems. He directed his warriors to fight only in self defense and not to instigate trouble. [33] In retrospect, the Nez Perces' parochial perspective of the war, and their failure to comprehend the scale and span of the United States government's resistance to their flight, became key ingredients in their ultimate tragedy.

In fact, the Nez Perces' movement was well known, having gone from frightening rumor to confirmed fact, and soldiers stationed near Missoula anxiously began preparations to receive them. These troops belonged to another administrative division—the Military Division of the Missouri, commanded from its Chicago headquarters by Lieutenant General Philip H. Sheridan. Within this vast military domain, the largest in the country, Montana Territory lay within the Department of Dakota, commanded by Brigadier General Alfred H. Terry from St. Paul, Minnesota. When the Nez Perces crossed the Bitterroots into Montana, they entered the department's District of Western Montana, commanded by Colonel John Gibbon from Fort Shaw. On word from Howard through Terry, it was Gibbon's soldiers who anticipated, and first encountered, the Nez Perces as they came east along the Lolo trail. [34]