Meanwhile talks between the Emir and the Russians produced a stalemate in October 1865. To force the issue, Chernyayev seized some Bokharan merchants then in Tashkent. In retaliation Muzaffar ordered the Russian diplomatic team arrested in November. Shortly afterward, all Russians in Bokhara were arrested.
Chernyayev had a new war. Intelligence discovered that while treating with the Russians, the Bokharans had been also entertaining envoys from Kokand, Khiva, Shahr-I-Sabz, and Afghanistan in an effort to form an anti-Russian coalition. Therefore on January 12, 1866 Chernyayev sent a small force across the Syr Darya at Chinaz. The Emir countered by massing his army near Samarkand and entering into serious negotiations with Khiva and the Turcomen nomads.
On the last day of January, 1866 Chernyayev took a large column across the frozen Syr Darya and marched against Djizak, a Bokharan frontier fortress and trade center which controlled access to the Zerashan Valley, the heart of the emirate. As he advanced the general sent a message to the Emir that he was not seeking to conquer Bokhara but simply sought the release of the captive Russian diplomats and traders. Further, the general said that he was marching on Djizak because this was the closest oasis to Bokhara large enough to service his troops.
The march on Djizak proved to be Chernyayev's undoing. The army camped about five miles from the oasis Attempts were made to buy firewood and hay but the local hakim rejected all offers. Chernyayev sent a small force to collect the denied supplies and the Bokharans fired on the foragers.
Short of forage and fuel, the Russians gradually realized that the Emir had no intention of releasing his prisoners Finally on February 11, 1866, after deciding not to assault Djizak, Chernyayev ordered a retreat to the Syr Darya. Unknown to him, three days earlier St. Petersburg had issued an order for his recall. Governmental disapproval of Chernyayev's thrust into Bokharan territory, Prince Gorchakov's frustration over getting the general to abide by government policy, the jealousy of N. A. Kryzanovsky, the new governor-general at Orenburg, combined to force him home in disgrace. Ironically, Chernyayev had been awarded a sword of honor only months earlier by the Tsar. Shernail was ignorant of his fate until the arrival in Tashkent of General D. I. Romanovskii, who informed Chernyayev that he was to assume command on the Syr Darya.
To make sure that the new governor of Turkestan would not have the freedom of action which his predecessor has assumed, Miliutin and Gorchakov, the Tsar's ministers of war and foreign relations issued Romanovskii a joint set of instructions. Unfortunately their orders were so broad and, at times, vague, the general was almost free to do as he pleased.
Thus when Romanovskii joined his command at Chinaz in March, 1866 and learned of the frequent skirmishes between Russians and Bokharans and of Emir Muzaffar's request to Khiva for help, he proposed to strengthen Russian's position in the region by weakening that of Bokhara. This he would do by seizing strategic villages and towns, hoping that St. Petersburg would be able to convince Britain and Persia of the necessity of such moves as well as his country' s peaceful intentions.
After receiving a Bokharan delegation demanding the withdrawal of Russian troops while avoiding the subject of the captive diplomats, Romanovskii started moving his column in early May, 1866. On May 6, with 3600 men, he routed a force of 5,000 Bokharan regulars and 35,000 Khazaks from an entrenched position near Irdzar. Muzaffar, who had commanded his troops in person, fled with the great bulk of his army, leaving over 1,000 dead on the field of battle. The Russian body count amounted to one dead and eleven wounded.
Instead of using the victory to secure the release of the diplomats and then withdrawing, Romanovskii decided to drive a wedge between Bokhara and its new vassal Kokand. Thus he turned his column up the Syr Darya. On May 14 Nau was entered without opposition. Ten days later the Russians stormed Khojend (Leninabad). At a cost of 5 killed, 122 wounded, and 6 missing Romanovskii controlled access to the Fergana Valley and a convenient staging point for further operations against either Bokhara or Kokand. A more immediate result of the battles at Irdzar and Khojend was the release of the diplomatic mission by the Emir in early June, 1866.
The summer of 1866 passed rather peacefully. There was a truce with Bokhara.