Unfortunately signing a peace treaty with the Russians did not end the problems of Kokand. When Nasir al-Din signed the treaty with Kaufman, his former associates saw this as an act of duplicity. Within a very short time, the rebellion flared anew. Soon the eastern provinces of Kokand and the city of Andizhan were in open revolt. Abd al-Rahman and Pulat Bey were welcomed in Andizhan and soon some 60,000 to 70,000 men had joined them.
The Russian commander at Namangan, Major General V.N. Trotsky marched o n the rebel city and besieged the insurgents there from September 30 to October 5, 1875. On the 5th, Trotsky ordered his men to storm the city. The assault proved premature. The rebel force put up such a stiff defense that the general called off the attack. Quickly thereafter the Russians lifted the siege and retreated toward Namangan. Trotsky's report stated that ten Russians had been killed and seventy wounded. Assault troops later interviewed insisted that casualties were actually four or five times the general's figures.
By October 9, Abd al-Rahman and Pulat Bey were in the city of Kokand and Nasir al-Din was on his way to Khojend. The rebels soon proclaimed Pulat Bey, whose real name was Ishak Mullah Hasan Ogly, the new khan. The Kokandians then pushed on to seize Marghilan and to threaten Trotsky's forces at Namangan.
At this critical time, Kaufman was ordered back to St. Petersburg. Thus M.D. Skobelev, recently promoted to major general for his services against Khiva and earlier in the campaign, found himself in command of a concentrating army at Namangan on October 16, 1875. Not one to remain idle, Skobelev took the bulk of his force into rebel territory and attacked the village of Tiura-Kurgan on October 23. The local rebels were defeated and the town was burned to punish the inhabitants for siding with the insurgents.
Other rebel forces were simultaneously moving against Skobelev's base at Namangan. The day after the destruction of Tiura-Kurgan, rebel forces occupied parts of Namangan and, with the help of the city's Uzbek and Tadjik population, attacked the small Russian garrison as well as a Russian camp outside the city. Despite intense pressure and huge odds, the garrison managed to keep control of the city's unfinished citadel and the troops in the encampment avoided being overrun throughout October 25 and 26.
Finally on October 27, Skobelev reappeared at Namangan. Lining up sixteen artillery pieces outside the city, he proceeded to shell those sections of Namangan known to be under rebel control. After a sufficient "softening" of rebel positions, Skobelev's infantry attacked the city, much of which had been destroyed during the artillery barrage. In his report, the Russian general claimed 3,800 rebels had been killed while the Russian loss was placed at six killed and 32 wounded. The victors turned residents and refugees out of the few remaining buildings and occupied them due to a lack of barracks space.
With his base secure, Skobelev marched into Kokandian territory in pursuit of Pulat Bey (now called Pulat Khan), Abd al-Rahman, and their confederates. For two months the Russians marched back and forth across rebel-held areas, turning much of central and eastern Kokand into a near-wasteland. Initially the Kokandians had attempted to resist, but after their army was crushed at Baligchi on November 11, the Kokandian leaders sought to avoid contact and fled to Andizhan.
Skobelev followed and shelled the rebel stronghold for a week early in January, 1876. Finally on January 8, the city surrendered. At a cost of two Russian dead and nine wounded, Skobelev had captured the rebels' center of resistance. The general reported that the Kokandian losses were "immense".
Even though the rebel heartland was occupied by the Russians, none of the rebel leadership had been seized. Thus Skobelev was quickly in the field again. Among the Kokandian rebels, the pressures of flight and the absence of any "sanctuaries" was beginning to wear on their will to resist.
After several more skirmishes, Abd al-Rahman Avtobachi and several other rebel leaders personally negotiated their surrenders with Skobelev. Considering the violence and brutality the general had used at Makram, Tiura-Kurgan, and Namangan, he was quite lenient with these rebel leaders. After they had placed themselves "at the mercy of the Tsar", all were pardoned.
While the Russian continued to search for Pulat Khan, Nasir al-Din reappeared on the scene. Under Russian protection in Khojend, he had received a delegation of Kokandian notables in early January, 1876. Their mission was to invite Nasir back to Kokand and to reassume the title and power of Khan. Early February found the exile eluding rebel forces and re-entering his former capital.
Unfortunately for Nasir, the Russian government had determined that the khanate was too politically unstable to remain in existence. Skobelev was ordered to occupy Kokand city. On February 19, 1876, the anniversary of his accession to the throne, Tsar Alexander II signed an order annexing Kokand to the Russian Empire. The new region was given the name Fergana, and Skobelev was named military governor.
As these events were transpiring, the military situation was moving toward an end. Skobelev's pursuit of Pulat Khan led the Russians to the fortress town of Uch-Kurgan, where the pretender had gathered some 5,000 supporters. After a lengthy bombardment, the Russian infantry stormed the town on February 28. Pulat Khan was found among the prisoners.
The pretender was not accorded the leniency given to his fellow conspirator Abd al-Rahman Avtobachi. It was known that Pulat Khan had killed a dozen Russian prisoners. There was also evidence that he had ordered the executions of women and family retainers of Khudyar Khan and Abd al-Rahman. Because of these crimes, the pretender was executed in March, 1886.