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Viceroy and struggle with Güyük

Withdrawing from Hungary, Batu made his camps along the banks of the Volga. When the Great Khatun Töregene invited him to elect the next Emperor of the Mongol Empire, Batu announced his inability to attend any immediate kurultai, thus delaying the succession for several years. Eventually, Güyük was elected Khagan in 1246, with Batu's brothers representing the Jochid lineage. As one of the oldest members of Chingisid Borjigin, Batu became a viceroy over all the western parts of the empire, controlling routine affairs among the Rus' princes, nominating Jochid retainers as governors of Iran, and receiving in audience grandees from the Caucasus. At no point, however, did he openly challenge the authority of the Great Khan.

During the absence of Batu, the Mongols who were left behind put to death Mstislav, the prince of Rylsk, in Kievan Rus'. On his return Batu summoned the Grand prince Yaroslav II of Vladimir to meet him. Yaroslav was well received by Batu, who confirmed him as suzerain over the other Rus' princes, and gave him authority of Kiev. The princes of Suzdal followed Yaroslav's example. Batu sent Yaroslav to the imperial court of Karakorum to assist at the inauguration of Güyük Khan in 1246. Plano Carpini, who got approval from Batu to go further, noted that the Great Khan's aunt was executed. At the same time Yaroslav was poisoned in Mongolia.

Batu had commissaries in the various towns where the dependent Rus' princes and other princes held their courts. The princes from Rus' principalities such as Vladimir Constantine, Boris, Gleb, Vasili, Constatantine, Vladimir Constantinovich, Vasil'ko and Sviatoslav Vsevolodovich of Vladimir, went to the court of Batu in person. When Michael of Chernigov, who had murdered the Mongol envoy in Kiev, arrived, the Mongol overseers were engaged in taking a census of the inhabitants for the poll tax. Michael was ordered to repair to Batu. When summoned before Batu, he was made to pass between two fires and ordered to prostrate himself before the tablets of Genghis Khan. According to the hagiographic vita written in praise of him decades later, Michael replied that he did not object to do obeisance to Batu himself, but to adore images of a dead man was repugnant. As he persisted in his refusal, Batu ordered his death.

Danylo of Halych was summoned to Batu in Sarai, and submitted himself to the Mongols, an act later decried in the Galician-Volhynian Chronicle, which otherwise glorified Danylo's exploits. Batu, addressing him, said "You have for a long time refused to come, but have effaced your ill conduct by your obedience" and saluted him with a draught of airag. They exchanged hostages whereby 100 families of Keraites were re-settled in Carpathian-Galicia. After the defeat of the Sultanate of Rum, Baiju freed David VII Ulu from Turkish imprisonment and sent him to Batu and Güyük. Fearing Baiju's aggressive policy, Queen Rusudan of Georgia sent her son David VI Narin to Batu's court to get official recognition as heir apparent. Batu supported David VI and granted him the rights above the Georgian and Armenian nobles and the Mongol tammachis. But Güyük made David Ulu the senior king of Georgia and ordered Batu's protege David Narin to be subordinate to David Ulu.

Suspicion between Batu and Güyük increased, and Güyük replaced the officials in Iran and the Caucasus with his own men, including Eljigidei. When Güyük began moving west, Sorghaghtani Beki, the widow of Tolui, warned Batu that he was actually the Great Khan's target. When Güyük summoned Batu to appear before him, Batu moved slowly. Before meeting Batu, Güyük died suddenly. According to William of Rubruck and a Muslim chronicle, one of Batu's brothers murdered or poisoned the Great Khan Güyük and Batu then killed the imperial envoy, though this account is not completely confirmed by other major sources.