The Apaches at San Carlos were thoroughly demoralized, hungry, and poorly clothed. They were also convinced that their agent, John Tiffany, was selling their rations to Americans off the reservation. Most of the Apaches realized that resistance was futile. so they turned to the Western Apache medicine man Noch-del-klinne as a prophet. He told his followers that if they held dances similar to the Ghost Dance , two dead chiefs would be resurrected and the whites would be driven away. As Noch-del-klinne's dances in the remote Cibecue Valley attracted more and more Apaches, General Eugene Carr at Fort Apache grew alarmed. In late August 1881, he organized an expedition of 117 troops to arrest the Apache leader. When he did, many of his Apache scouts rebelled. Shots were fired, people scattered, and both soldiers and Apaches were killed, including Noch-del-klinne. It was the only time during the history of the Apache Wars that Apache scouts turned against U.S. troops.
Crook believed that the scouts had been provoked and argued that "any attempt to punish any of the Indian soldiers for participation in it would bring on war." The army still court-martialed five of the scouts who surrendered anyway, sending two to the military prison of Alcatraz. The other three, Sergeant Dandy Jim, Sergeant Dead Shot, and Private Skippy, were hung at Fort Grant on March 3, 1882.
Many at San Carlos thought the army intended to punish them as well, so Juh, Chato, Naiche, Geronimo, and 66 other members of the Nednhi band slipped away in September 1881. For the next four years the Chiricahuas and their pursuers fought a war of attrition, most of it on Mexican soil. In the winter of 1882, Juh ambushed and killed a party of Mexicans led by the veteran Indian fighter Juan Mata Ortiz, Terrazas's second-in-command at Tres Castillos. The following year, Chihuahuan militia surprised Juh's camp and killed his wife and daughter. Sometime after that, Juh's horse slipped on a steep mountain trail above the Ríos Aros in northwestern Chihuahua, tumbling the chief into the water. Although other Chiricahuas tried to revive him, he never regained consciousness. From then on, Geronimo led most of the Chiricahuas who refused reservation life.
Geronimo's principal opponent was Crook, who returned to take over the Department of Arizona in 1882. On July 29, Mexico signed a treaty allowing U.S. troops to chase hostile Apaches across the international boundary. In May 1883, Crook gathered about 50 soldiers and 200 Quechan, Mohave, and Apache scouts and rode up the rugged valley of the Bavispe River in the northwestern Sonora until he turned east into the Sierra Madre. Captain Emmet Crawford and his scouts were the first to encounter the Chiricahuas, attacking the ranchería of Chato and Bonito, which turned out to be the only hostile engagement of the entire campaign. The penetration of their territory by U.S. troops was threat enough, and soon the Apaches, including Geronimo, made their way to Crook's camp in the Sierra Madre.
For the next several days, Crook and Geronimo sparred with each other for several days over the details of the surrender. Crook realized if he insisted complete submission, the Apaches would scatter into the mountains and the war would drag on for years. He accepted Geronimo's promise to return to San Carlos on his own, a move that prompted critics to charge that Geronimo had captured Crook rather than vice versa. Crook then led Nana, Loco, Bonito, and 225 other Chiricahuas back to Arizona, arriving at San Carlos on June 23.
Confounding the skeptics, Geronimo kept his part of the bargain in late February 1884. He and the other Chiricahuas settled along Turkey Creek 15 miles (24 km) below Fort Apache, where they cultivated 4,000 acres (16 km²) and harvested 3,850,000 pounds (1,750,000 kg) of corn, 600,000 pounds (270,000 kg) of wheat and other cereals, 540,000 pounds (240,000 kg) of beans, 20,000 pounds (9,000 kg) of potatos, and 200,000 pumpkins. Still, the officers at Fort Apache clashed incessantly with the agents at San Carlos. Accusations of corruption kept surfacing with the agents at San Carlos. Accusations of corruption kept surfacing, and in May Crook prohibited alcohol on the reservation, outlawing the brewing of tizwin , a fermented corn liquor favored by the Apaches. Under the guise of preventing wife beating, the military also began to interfere in the personal affairs of Apache families themselves. On May 15 the Chircahuas demonstrated their contempt by getting drunk on tizwin and flaunting their disobedience. Two days later, Geronimo, Naiche, Nana, and 131 other Chiricahuas deserted the reservation.
Crook organized another expedition into northern Sonora, and once gain Apache scouts, including former Chiricahua rebelts like Chato, led the way. The general and Geronimo sat down in a cottonwood-shaded ravine called Cañon de los Embudos on March 25, 1886. Crook's superiors wanted unconditional surrender. The Chiricahuas wanted an immediate return to San Carlos. Crook and Geronimo agreed to a compromise that would have allowed the Chiricahuas to return to the reservation after a two-year imprisonment back east, but as soon as General Phillip Sheridan and President Grover Cleveland learned of the agreement, they rejected it. By then, Geronimo, Naiche, and forty other Chiricahuas, including 14 women and six children, had slipped away.
When Sheridan heard that the peace talks had collapsed, he concluded that the Apache scouts had allowed Geronimo to escape and told Crook to use regular troops from then on. He also ordered Crook to load the rest of the Chiricahuas onto railroad cars and ship them to Fort Marion (now Castillo de San Marcos National Monument) in St. Augustine, Florida with no promise of return. Crook asked to be relieved.
His successor was General Nelson Miles, who was given 5,000 soldiers, one-fourth of the entire U.S. army, to capture or kill Geronimo's little band. Miles deployed his regulars and and erected twenty-seven heliograph stations to keep track of the hostiles. Two Chiricahua scouts under Captain Charles Gatewood, Kayitah and Martine, tracked Geronimo to the Torres Mountains southeast of Fronteras. Gatewood met with the Chiricahua leader in late August and persuaded him to surrender for the fourth and final time. Geronimo did so at Skeleton Canyon in the Peloncillo Mountains on September 4, 1886.