As the tribesmen of Joseph, Ollokot, White Bird, and Toohoolhoolzote bypassed the soldiers at Cottonwood and crossed Camas Prairie to the South Fork of the Clearwater River, warriors from their company raided abandoned farms and ranches, continuing the pattern established at the start of the outbreak. A number of forays occurred on the prairie, but the most damaging were those to homesteads along the Clearwater, where the warriors plundered and burned houses, barns, and outbuildings. On Camas Prairie, ten miles from Mount Idaho, Henry Croasdaile's house was "completely gutted & torn to pieces inside, all the furniture, bedding, blankets, [and] groceries . . . stolen or broken up." James C. Cearley, who had fought with Randall's men near Cottonwood, lost his barn, while John Flynn and John Healey reported that the Nez Perces "burned our House, Barn, shedding, & all our clothing & provisions." The home of D. H. Howser, who had died of wounds following the volunteers' engagement, was burned on July 6, and farmer J. C. Harris reported that the tribesmen had ruined sixteen acres of wheat and timothy at his place. Along the South Fork of the Clearwater River, the Nez Perces burned houses and barns and destroyed fences and crops belonging to George Dempster, D. M. Jones, William Grotts, James T. Silverwood, Thelbert Wall, and Arthur Williams. 
After diagonally traversing the country between Cottonwood and Grangeville, the Nez Perces followed the narrowing canyon of Cottonwood Creek to its mouth, at last setting up their village on the South Fork of the Clearwater River. The large camp occupied both sides of the stream, but mostly straddled the ground on the west side. There the refugees from Looking Glass's destroyed village met them about July 7, bringing their number to approximately 740 men, women, and children. On the eighth, possibly in preparation for moving east across the Bitterroot Mountains, the Nee-Me-Poo forded many of their animals to the north side of the Middle Clearwater. At about the same time, many people in the Clearwater camp rode over to Kamiah and crossed the middle fork to attend a Dreamer service. 
It was after the tribesmen had established their village on the banks of the South Fork that the reorganized battalion of volunteers found them. Colonel McConville had left Mount Idaho with seventy-five men on the morning of July 8 after receiving ammunition from Howard's command at the mouth of White Bird Creek.  McConville's command crossed to Cottonwood Creek, then followed that stream until dark and unknowingly camped a short distance from the village. During the night, picket guards informed McConville of the proximity of the Nez Perce village less than a mile away, and the colonel dispatched a rider, John McPherson, to notify Howard of the discovery. McConville sent ten of his men to a high hill about one-half mile away, directing them "to hold the hill at all hazards, and to give the alarm in case of the approach of the Indians."  Presently, two more volunteers, George Riggins and P. C. Malin, rode off to Mount Idaho to find Howard. Before daylight, two of McConville's men, Lieutenants Luther P. Wilmot and James Cearley, reconnoitered the Nez Perce camp, approaching to within one-half mile of the village. As Wilmot recalled:
After a thorough discussion, the men decided to stay put and after dark get word to Howard and to assist the army troops in an attack.  But on the afternoon of July 9, the inadvertent discharge of a rifle by one of McConville's men brought instantaneous attention from the Nez Perces and changed the plan.  As the warriors responded, McConville and the balance of his command filled kettles and canteens with water and joined the lookouts on the hill in raising rock fortifications. "It was flat on top," recalled Wilmot, "and one of the finest places any one could wish to make a stand." 
For the next day, Nez Perce warriors surrounded and isolated McConville on the hill, which became known alternately by the appellations, "Misery Hill," "Mount Misery," or "Fort Misery." Climbing an adjacent ridge, the warriors began the confrontation by verbally challenging the men to fight. Near midnight, they "suddenly burst forth [with] a succession of the most unearthly yells, screeches, and screams of wild birds, among which were distinguishable the notes of the curlew . . . , the bark of the prairie wolf, [and] the scream of the panther."  Then, at 1:00 a.m. on July 10, they opened a "strong fire" against the volunteers, keeping it up until dawn.  During the night, they stampeded the men's horses, capturing forty-three animals. At 7:00 a.m., the Nez Perces opened a mocking dialogue, then formed themselves in a line ready to attack. But suddenly they pulled back and returned to the South Fork.  McConville's men waited on the hill until late in the afternoon when they saw thirty of the warriors move upstream to attack a small party of volunteers coming from Mount Idaho under the battalion's major, George Shearer. McConville directed Wilmot and twenty men forward, and they headed off the warriors, shooting one and killing a pony, after which the tribesmen pulled back, allowing Shearer's party to reach Misery Hill. McConville learned from Shearer that Howard had crossed to the east side of the South Fork. (Howard had attempted to contact McConville, to tell him to "be encouraged and keep all the brave men you can, barricading your position if necessary," but the presence of the Nez Perces had prevented his couriers from reaching McConville's camp. ) Late that day, Adjutant Morris of the volunteers drafted the following for delivery at Mount Idaho:
After Shearer's arrival, McConville sent Wilmot and Benjamin Penny to find Howard and coordinate with his force. It was agreed that, if Howard attacked the village the next day, Wilmot was to signal the action with a bonfire. Wilmot reached Howard that night, and the next day, he rode to Mount Idaho before starting back to McConville.  Meanwhile, on the morning of July 11, the warriors seemingly distracted and his men low on provisions, Colonel McConville led them afoot out of their hilltop fortifications. They halted for the night at Cearley's ravaged property, and on the twelfth, his men mounted on animals obtained from the citizens of Mount Idaho, McConville reversed direction on word from Howard that the Nez Perces were withdrawing toward Kamiah. The movement to contain the Nez Perces south and west of Howard's position occupied the volunteers over the succeeding two days. 
Few Nez Perce accounts discussed the skirmishing at Misery Hill. Yellow Wolf stated that the place was named Possossona (Water Passing), that the fighting occurred sporadically, and that the warriors departed after sundown. They returned later, but the volunteers did not prevent them from capturing the horses, which Yellow Wolf identified as having been stolen from Looking Glass's camp. "We took them all, except a few we did not want," he said, describing the shooting in the darkness as "just like fireworks." According to the Nez Perces, only one warrior received injury in the fight with McConville's volunteers. He was Paktilek, who lost his right-hand forefinger as he made off with two ponies. 
By his withdrawal from Misery Hill on July 11, McConville lost all chance of coordinating with General Howard in an attack on the Nez Perce camp. On the ninth, Howardinformed of the location of the Nez Perces and now accompanied by Perry's cavalrystarted north, intent on following "Whipple's route to Looking Glass's camp via Jackson's Bridge, with the hope of taking the enemy in reverse."  Therefore, he went on to Thelbert Wall's burned ranch,  four miles beyond the bridge and on the east side of the South Fork of the Clearwater, where he went into bivouac. There he awaited the arrival of his exhausted artillery/infantrymen who had to be transported from the Salmon River in wagons sent down from Grangeville and who reached camp at about 8:00 p.m. At Wall's, most of the men bivouacked on a high hill beyond the burned buildings. Before daylight on the tenth, Howard's restive pickets opened fire on each other, but no one was hurt. The command laid over, still awaiting the artillerymen. 
At 7:00 Wednesday morning, July 11, the command, numbering 350 men and guided by local resident James T. Silverwood and a contingent of scouts headed by Arthur ("Ad") Chapman,  at last moved out together along the high ground between the forks of the Clearwater, their left flank generally paralleling the South Fork.  The cavalry battalion, composed of four companies of the First Cavalry commanded by Captain David Perry, led the way, followed by that of the foot soldiers, five companies of the Twenty-first Infantry under Captain Evan Miles, and the artillery, acting as infantry, comprised of five batteries (companies) of the Fourth Artillery under Captain Marcus P. Miller. Following the artillerymen came two howitzers and their crews, commanded by Second Lieutenant Harrison G. Otis of the Fourth, and the two Gatling guns and their attendants.  Besides the civilian guides, several newspaper correspondents also went along, representing such tabloids as the Portland Oregonian, San Francisco Chronicle, Portland Standard, and Idaho Tri-Weekly Statesman out of Boise.
Captain Trimble's Company H, First Cavalry, had the honor of leading the advance guard, with six mounted troopers at the very front of the column. The day was clear and breezy, not yet hot. The army kept to the high ridges, marching in column on ground nearly one thousand feet above the bottomlands of the South Fork, and heading in the direction of Looking Glass's former camp at the mouth of Clear Creek on the Middle Clearwater. A few miles out, the troops came upon a small group of horses, mares and colts that Chapman identified as having been stolen from his ranch on the Cottonwood. At this sign of the possible proximity of Indians, skirmishers deployed and the advance resumed. At about 11:45 a.m., as the cavalry passed over a long crest leading toward Clear Creek, Howard's aide, First Lieutenant Robert H. Fletcher (Twenty-first Infantry), and Scout Chapman, while reconnoitering along the bluffs, peered down from the height and first observed the large Nez Perce village at the mouth of Cottonwood Creek. They were quickly joined by another aide, First Lieutenant Melville C. Wilkinson (Third Infantry), along with Captain Trimble, Silverwood, and several others. A newspaper correspondent described the sight:
A very pretty scene met our view. The ranches looked fresh and fertile, the dingy rivernow not worthy the name of "Clearwater"only served by its ugliness to heighten the effect by contrast with the gardens, dotted here and there along the river bank. The company soon sighted the enemy on a flat, hedged in on the river by a dense underbrush, with a few pine trees interspersed on the flat. About, the hills rose steep, making it equally as good a place for attack as for defense. 
Informed of the discovery, General Howard rode to the bluff and saw the village, which stood about one mile southwest of his position. The Indians had already sighted the command, and the officers watched as they herded their livestock upstream and away from the camp. After deciding that they were not reservation Nez Perces, Howard ordered a howitzer brought forward and placed on the bluff overlooking the South Fork. (This bluff is immediately north of what today is called Stites Canyon, down which a modern road leads to the community of Stites.) The gun, overseen by Captain Lawrence S. Babbitt, Howard's ordnance officer and acting aide, and commanded by Lieutenant Otis, quickly opened against the rapidly emptying Indian village. But because the distance was too great, the howitzer shells burst high in the air and did no damage beyond frightening the fleeing people.  After ten minutes, Howard directed that both of his howitzers, along with the two Gatling guns, supported by Captain Winters's Company E, First Cavalry, and Captain George H. Burton's Company C, Twenty-first Infantry, be shifted to another promontory on the bluff to the south and across a large ravine (present Stites Canyon) leading to the river bottom. While the distance was but a half mile on a straight line, the defile (termed by Howard "a deep and rocky transverse ravine") necessitated a detour of one and one-half miles around its head to reach the bluff where the pieces were then deployed. At Howard's direction, Captain Miller sent Trimble and his company ahead down the river to reconnoiter.