As stated, the Nez Perces entered the national park via the Madison River Valley on August 22, the day that Howard camped along the Henry's (or North) Fork of the Snake River en route to Henry's Lake. On Thursday, August 23, Howard's scout, Fisher, led his Bannocks through Targhee Pass into the Madison River Valley. Atop the Continental Divide, Fisher espied the Nez Perce camp along the Madison River; a short time later his scouts encountered their trail. Reaching the South Fork of the Madison at sundown, Fisher halted his scouts, sending forth a few who returned shortly to report that the Nez Perce camp lay but a few miles away, and that it could be taken easily by the Bannocks. After some deliberation, Fisher acceded in the plan, fearing that the cavalry could not arrive in time to surprise the camp. Yet after all proper dispositions were made, including the Bannocks readying themselves for an assault, several of the scouts returned to report the camp deserted, and the offensive plan collapsed entirely. 
Besides the Nez Perces, the Bannocks, as well as other tribes of the Great Basin and Plateau, had since the 1830s journeyed through what became the national park to the Montana plains to hunt buffalo. The standard route, known by the 1870s as the Bannock Trail, started at Camas Meadows and, moving east, crossed Targhee Pass and the basin of the Madison River. It then penetrated the Gallatin Mountains to the vicinity of Echo Peak and passed down Indian Creek to the Gardner River. The trail then led through Snow Pass, reaching Mammoth Hot Springs before continuing up Lava Creek and across Blacktail Deer Creek Plateau to the Yellowstone and the East Fork of the Yellowstone. It then proceeded up the East Fork Valley, branching to enter the Absaroka Range and emerge in the valley of Clark's Fork, from which place its users might travel to the Yellowstone Valley or Wyoming Basin.  In 1877, however, the Nez Perces chose not to follow the Bannock Trail, instead opting to pursue a hunting trail with which they were largely unfamiliar. The reason for this decision is not altogether clear; perhaps it was meant to confuse the army, or possibly the tribesmen were wary of troops operating in the northern reaches of the park.
The Nez Perces did not tarry long at the site on the Madison River subsequently located by Fisher and his scouts. In one of his accounts, Yellow Wolf indicated that late in the day "the Indians were getting ready to move camp." It was soon after that that Yellow Wolf and Otskai, roaming several miles away from that camp, happened on fifty-two-year-old John Shively, a prospector who was crossing the park from the Black Hills gold country in Dakota Territory. As Shively ate supper late that day in the Lower Geyser Basin, the Indians approached him. (Shively maintained that four warriors approached him while at least twenty more surrounded him at a distance.) Taken to the Nez Perce camp, Shively attended a council of the leaders in which "they asked me if I would show them the best trail leading out of the park to Wind River, where they were going." Fearing for his life, the miner replied affirmatively. Later, Shively learned that the Nez Perces had taken that route rather than the customary Bannock Trail "to get away from Howard." The warriors then detained Shively for several days, until the night of September 2, when he managed to escape. 
Although Fisher noted in his journal that the Nez Perces' presumed camp (that he found abandoned) was on the Madison, "a few miles above us," and "on the opposite side from where we were," in fact, as indicated by Yellow Wolf and as discovered by Fisher, the tribesmen had broken that camp and gone on late in the afternoon, and that Yellow Wolf had gone in advance "about six miles" before encountering Shively. Actually, Yellow Wolf and the tribesmen had to have traveled much farther to camp along the Firehole River in the area of Lower Geyser Basin, where Shively was and where he said the Nez Perces camped. If Fisher spotted the abandoned camp of the Nez Perces only a few miles from his position on the South Fork of the Madison, it seems that the tribesmen traveled up the Madison all the way to the Firehole and then covered the distance to Lower Geyser Basin, a total distance of around ten miles, all before darkness fell. 
Determining the subsequent course of the Nez Perces through the west and central areas of the park becomes easier after August 24, for on that day they encountered the tourists from Radersburg, Montana. Yellow Wolf claimed to have seen lights from their campfire on the night of the twenty-third, but decided to wait until morning to investigate because of boggy ground over which they must proceed. (A wise decision, considering the many hot springs in the area.) Early the next day, the Nez Perces surprised the group of seven men and two women as they prepared breakfast, and, as discussed below, over the succeeding two days the fate of its various members hung in the balance. Some of the party escaped relatively quickly, and some were found by Howard's troops and scouts as they fled for safety.
That day, August 24, the Nez Perces passed from the Firehole River up the East Fork of the Firehole (later designated Nez Perce Creek), ascending Mary Mountain and skirting Mary Lake (about one-half mile long, north to south, and one-quarter mile wide) and Hot Sulphur Springs (today Highland Hot Springs) on the Central Plateau. They camped along the edge of a basin about three-quarters mile in circumference, inside which their immense horse herd grazed.  On Saturday, the twenty-fifth, they continued down the slope and through Hayden Valley and along Elk Antler Creek to the Yellowstone River, fording the stream above the Mud Volcano, about five miles north of Yellowstone Lake (the crossing is known today as Nez Perce Ford), and camping on the east side of the river. Here the Nez Perces released the remaining tourists, providing them with food, horses, assistance in recrossing the river, and directions toward Mammoth Hot Springs far to the northwest.
Earlier that day, as they passed through Hayden Valley, the warriors had captured a recently discharged soldier, James C. Irwin, from Fort Ellis and still in uniform. His sojourn with the Nez Perces lasted six days until September 1, when he managed to escape. Across the Yellowstone River, they continued south, crossed Pelican Creek, and camped near a pool on the north shore of the lake later named Indian Pond. There the people, aware of Howard's location at Henry's Lake far in the rear, evidently passed two days without concern of the soldiers, leaving on the morning of August 28 to ascend winding Pelican Creek east and north. By then, Fisher's Bannocks (numerically reduced to forty after the departure of fifteen deserters) were in close pursuit, having crossed from Lower Geyser Basin on the twenty-sixth and reached Mud Volcano on the twenty-seventh, where they killed and scalped an elderly Nez Perce woman who had stayed behind so as to not hinder the progress of her people. Fording the Yellowstone the next day, Fisher approached the camp site in the timber near Yellowstone Lake, but was too late to find the Indians. 
Scout Fisher's journal of his reconnoitering of the main Nez Perce caravan on the days after August 28, together with the account of John Shively, who remained with the caravan following his capture, provide the only known contemporary evidence that enable the approximate tracking of those people until the time they left the national park. The following estimate of the course of the tribesmenwho could have traveled through the park in more than one groupis based on these sources, on period cartographic information, and on previous judgments of that course. Regarding the cartographic data, it is important to note changes in Yellowstone Park nomenclature since the time of the Nez Perces' passage. Specifically, Pelican Creek, as referenced on the Hayden Survey Map of 1878, is today called Raven Creek. In 1877 and 1878, the stream known as Pelican Creek trended generally north and east from Yellowstone Lake and passed to the east of "Pelican Hill" (now Pelican Cone). The only major affluents of Pelican Creek shown on the 1878 map were "Lake Creek" (present Astringent Creek) and "West Pelican Creek" (today's main Pelican Creek), both joining the major stream from the north. Smaller, unnamed tributaries also lead into the primary stream from the southeast. Furthermore, by 1878 a trail paralleled Pelican Creek for much of its length and beyond its headwaters, passing near or across the heads of several tributaries (particularly Timothy Creek) of the East Fork of the Yellowstone (Lamar River).  Shively's recollections, given but a few days after his escape from the Nez Perces, are not altogether clear on details of where the people were at different points. Based on his detailed interview account published in the Deer Lodge New-Northwest, his role as guide was briefly usurped by a Shoshone chief (probably Little Bear). On August 28, according to this account, the tribesmen followed the Shoshone, apparently continuing up Pelican Creek, but then bearing left toward the Yellowstone River and going "around a mountain" before correcting their course and emerging on the East Fork. In reaching the East Fork, the Nez Perces might have descended Timothy Creek. In any event, on the thirtieth, according to Shively, they moved down the East Fork "four or five miles towards Baronette's Bridge" at the junction of the East Fork with the Yellowstone, but on the thirty-first, going on, they decided to send scouts some twenty miles to the bridge, which ultimately was burned at the direction of the Shoshone leader. According to Shively, the Nez Perces "did not like the idea of coming down that stream." Possibly because of potential confrontations with troops or miners, they turned back "to seek an outlet toward the Big Horn." Still on the thirty-first, the Nez Perce council reconvened, and Shively, now reinstated, told them he could guide them to Clark's Fork River and scouts were sent to explore that area. 
Fisher's journal, while otherwise spotty and unclear on many points, precisely mentioned Pelican Creekno forks or subordinate affluentsas the stream he ascended during his scout after the Nez Perces. On August 28, he followed their trail up Pelican Creek for "about ten miles," then climbed a mountainside from which he "could plainly see the smoke in the enemy's camp."  From this point, Fisher turned back, not to actively resume his reconnaissance until September 1, when he and a group of scouts started up Pelican Creek on the trail again. At sundown that day, they suddenly encountered the discharged soldier, Irwin, who said he had left the Nez Perce camp that morning "about thirty miles from here." According to Fisher's dispatch to Howard, the encounter with Irwin happened three miles up Pelican Creek:
Next day, as Fisher resumed his probe, Irwin started for Howard's command. On arrival September 2, he told the general that the tribesmen were no more than forty miles away, "having been lost for several days in the pine forests." Irwin further said that there were 216 warriors, "besides boys and squaws, who use guns at times of battle." Poker Joe (Lean Elk) had assumed a major leadership role and was apparently so familiar with Virginia City and Bozeman that "he sent word by Irwin to a man named Kennedy to look after a house and lot of his at the latter place." Evidently misconstruing Joseph's designated role with the noncombatants of the train, Irwin reported that he had been "supplanted" as chief and spent his time "packing mules and building fires." The leaders had sent four emissaries to the Crows to try to gain their support; meantime, the people were well supplied with dried meat, sugar, and ammunition, but lacked flour, salt, and coffee. Finally, Irwin told of Shively's captivity among the Nez Perces working as a guide. 
Meanwhile, Fisher continued up Pelican Creek on September 2, but did not start until late afternoon, after having taken some observations from a mountainside and then gotten delayed in "swamps and fallen timber" which retarded his party's advance. "We made about six miles over a very bad trail through fallen timber," he noted in his journal. Yet the scout recorded that he and his Bannocks crested the Pelican Creek divide to reach the waters of the East Fork of the Yellowstone River.  Based on the cartographic data cited above, the "waters" could logically have been the upper reaches of Timothy Creek, the headwaters of which extended sufficiently westward to bisect the trail shown on the Hayden map, and the course of which leads naturally northeast to the East Fork. On Monday, September 3, the scouts followed the trail "through the roughest cañon I ever undertook to pass through," wrote Fisher.
While other creek bottoms might more directly align with Fisher's description, that of Timothy Creek also conforms well, according to observations by park authorities who have studied and hiked over the terrain. 
On the fourth, Fisher and a white scout named A. K. Gird ascended to "the divide" and by noon had approached within a mile of the Nez Perce village, which was in process of breaking camp"gathering their horses together and pulling their lodges down preparatory to leaving."  The "divide" was perhaps the high ridge on the south side of Miller Creek, separating that stream from the East Fork (Lamar) River, and reached by climbing the canyon wall directly east of the East Fork, from which point the upper Miller Creek drainage could be observed below and to the east. According to Fisher, the Nez Perces then traveled "nearly east" up the canyon. The Bannocks told Fisher that the area was called the "trap" and that "there is no way of getting out of it except at each end and that it is about fifteen miles long."  In fact, the area of upper Miller Creekwith its exit-impeding features as noted by modern hikersconfigures well with reference to a "trap."  That afternoon, Fisher and his colleagues heard gunfire in the canyon below. They tried to descend to the bottom, but found the canyon edge to be perpendicular and impossible to negotiate. Later, they learned that some of Fisher's Bannocks had accidentally run into a rearguard of some forty Nez Perces and had a brisk exchange in which "at least a hundred shots were fired." They reported having killed one Nez Perce.  It is hypothesized that, from the "trap" of upper Miller Creek, the people continued east to a grassy summit near the headwaters of Miller, Papoose, and Hoodoo creeks known as Hoodoo Basin. John Shively reported that the tribesmen camped on "a beautiful, grassy ridge" east of Yellowstone Lake that conceivably could be the same area. (It was from this place that Shively, after pointing the Nez Perces in the direction of the Crow country, made his escape on the night of September 2. ) Park superintendent Philetus W. Norris noted in 1880 that he had found the remains of numerous Indian lodges, some of which were still standing "near the summit of an open, grassy pass between Hoodoo and Miller Creeks."  And while the lodge poles might have been left there by other tribes, the location aligns well with the presumed route of the Nez Perces as they headed toward Crandall Creek on Clark's Fork River.
On September 6, Fisher's party traveled from their camp on the East Fork twelve miles "down the stream over an exceedingly rough trail." He wrote: "The enemy's trail followed down the same creek that we came down today to a point where it formed a junction with another stream and then turned in a south of east direction, making up this last mentioned creek. Following their trail upward, we came upon some cattle they had killed."  This imprecise entry  suggests that Fisher's reconnaissance on September 4 failed to detect the departure/return of a Nez Perce scouting party down the East Fork to Baronett's bridge and that the bands likely were traveling in more than one group. Fisher's comments indicate that a major group of Nez Perces apparently turned right up Calfee Creek or Cache Creek, probably the latter, then turned southeast up South Cache Creek, or traveled along the divide between Calfee and Cache creeks, either to rendezvous with the other groups on the grassy slopes near Papoose Creek or to pass east down Timber Creek to Crandall Creek.  Fisher's scouts followed the trail an unspecified distance and discovered the butchered cattle identified as having been slaughtered by the Nez Perces seemingly because of their practice of taking small quantities of meat (particularly internal organs) and leaving the carcasses mostly untouched.  Then the scouts eventually moved three miles to Soda Butte Creek, and after going two more miles they made camp. "There is just an even dozen of us now," wrote Fisher of his dwindling scouting force as more of the Bannocks departed.  On the seventh, Fisher caught up with Howard's command, which had preceded him up Soda Butte Creek and out of the national park.