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Some historians attribute the order to the government in Moscow, specifically Yakov Sverdlov and Vladimir Lenin, who wished to prevent the rescue of the Imperial Family by the approaching Czechoslovak Legion (fighting with the White Army against Bolsheviks) during the ongoing Russian Civil War. This is supported by a passage in Leon Trotsky's diary.
The February Revolution saw the abdication of Nicholas II. Afterwards he and his family were placed under house arrest by the Provisional Government. They were first confined to their palace in Tsarskoye Selo.
Uncomfortable with the ex-czar and his family still living in Petrograd, Prime Minister Aleksandr Kerensky had them relocated to Tobolsk in August 1917. After the Bolshevik Party seized power, the conditions of their imprisonment grew stricter. Nicholas was no longer allowed to wear any medals or regalia, all but their doctor and two servants were sent away, and they had to eat their meals from a common pot. Demands to put the deposed ruler on trial grew increasingly frequent.
In April 1918, the Romanovs were transferred to a townhouse in the Ural mining town in Ekaterinburg originally owned by a man called Nikolai Ipatiev. The Cheka rechristened the building with the foreboding title "the House of Special Purpose".
Due to a lack of skilled lawyers for jury and threat of the Czech Legion attempting to free the Romanovs, Lenin decided to murder them without trial. It was feared that the family would be a rallying point for the Whites, so they were to be killed in for national security purposes.
Around midnight on July 16, Yakov Yurovsky, the commandant of The House of Special Purpose, ordered the Romanovs' physician, Dr. Botkin, to awaken the sleeping family and ask them to put on their clothes, under the pretext that the family would be moved to a safe location due to impending chaos in Ekaterinburg.
The family was led into the cellar, with the sound of a running truck giving ambiance. They were told that they were going to have a photograph taken as evidence that they were alive. Three chairs were put out: one for Nicholas, another for Alexandra, and a third for Alexis, who was so ill at that point that his father had to carry him downstairs. Yurovsky read out their death sentence that, he said, had been passed by the Ural soviet.
Nicholas was shot dead and the rest of the family were shot soon after. Alexis didn't die immediately, and Yurovsky had to empty his revolver into the boy. The girls were harder to kill due to the sizable amount of diamonds sewn into their clothes. Anastasia, the youngest of the duchesses, didn't die immediately, but was finished by a bayonet.
The corpses were taken by truck to a local mine, called the Four Brothers, where they were stripped, hacked to pieces, and burned with kerosene. When the truck broke down on the way to the next chosen site, Yurovsky made new arrangements, and buried most of the scorched bodies in a pit sealed and concealed with rubble, covered over with railroad ties and then dirt on Koptyaki Road, a cart track twelve miles north of Ekaterinburg.
Yurovsky returned to Moscow on July 18. One week later, the Czechs occupied Ekaterinburg.
Initially, the Bolshevik government denied that the Romanovs were dead, claiming that they had been relocated to a classified location. The Whites, on the other hand, had no doubts that Nicholas and his family were dead. They would not be alone. Every Romanov the Bolsheviks found would be murdered throughout the era of Red Terror.
When Ekaterinburg was taken by the Whites, an investigation led by Nikolai Sokolov was held in the surrounding area. Traces of the murder were found immediately, but the bodies weren't. Ganya's Pit at the Four Brothers' mine, the location where the bodies and clothing were allegedly destroyed, was thoroughly searched and yielded a wealth of artifacts.
In a clearing known as the Pig's Meadow, four miles from the Four Brothers mine, nine bodies were unearthed in a single pit. They were identified as Nicholas, Alexandra, Grand Duchesses Olga, Tatiana, and Anastasia, Dr. Botkin, and the three servants who joined them in exile. A second, smaller pit containing two bodies, those of Crown Prince Alexis and Grand Duchess Maria, was uncovered to the south of the others.
After the defeat of the Reds, many surviving leaders were tried for war crimes at Odessa. The killing of the Romanovs was one of many things discussed.
Lenin, Trotsky, and Sverdlov had made out a plan to empower the Ekaterinburg soviet to execute the family. A number of fabricated plots and rescue attempts were used as justification. One executioner, Filipp Goloshchyokin, had visited Moscow twice before the shooting, both times to meet with Lenin, Sverdlov, and others. It became clear, as far as the court was concerned, that Lenin had pre-planned the execution and had been astute in covering his tracks. The Soviet ambassador to Germany, Adolf Joffe, was asked, from the kaiser down, about Nicholas' fate; he was told nothing. When Cheka founder Felix Dzerdzhinsky was in Berlin sometime later, Joffe asked why he wasn't notified. According to Dzerdzhinsky, Lenin had ordered the execution and that it would be easier to lie about it to the German nobility.
Yurovsky was ultimately acquitted by the court and exiled to Norway. He would later die of a heart attack in Hammerfest in 1938.
On May 11, 1921, the bodies of the seven Romanovs and four retainers proceeded through the streets of Petrograd and to the Peter-and-Paul Fortress, final resting place of every Russian monarch since Peter the Great. Various Romanov relatives attended the ceremony such as Czar Nicholas III, the former czar's uncle, and King George V of England.