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Imprisonment

Joseph Stalin 's Great Purge severely damaged RNII, with Director Kleymyonov and Chief Engineer Langemak arrested in November 1937, tortured, made to sign false confessions and executed in January 1938. Glushko was arrested in March 1938 and with many other leading engineers was imprisoned in the Gulag. Korolev was arrested by the NKVD on 27 June 1938 after being accused of a variety of charges, including false charges extracted from Kleymyonov, Langemak and Glushko. He was tortured in the Lubyanka prison to extract a confession. Glushko and Korolev had reportedly been denounced by Andrei Kostikov who became the head of RNII after its leadership was arrested.

Korolev was sent to prison, where he wrote many appeals to the authorities, including Stalin himself. Following the fall of NKVD head Nikolai Yezhov, the new chief Lavrenti Beria chose to retry Korolev on reduced charges in 1939; but by that time Korolev was on his way from prison to a Gulag forced labour camp in Kolyma in the far east of Siberia, where he spent several months in a gold mine before word reached him of his retrial. Work camp conditions of inadequate food, shelter, and clothing killed thousands of prisoners each month. Korolev sustained injuries, including possibly a heart attack and lost most of his teeth from scurvy before being returned to Moscow in late 1939. When he reached Moscow, Korolev's sentence was reduced to eight years. However, due to the intervention by his old mentor, Andrei Tupolev, he was relocated to a prison for scientists and engineers in September 1940. These were labor camps where scientists and engineers worked on projects assigned by the Communist party leadership. The Central Design Bureau 29 (CKB-29, ЦКБ-29) of the NKVD, served as Tupolev's engineering facility, and Korolev was brought here to work. During World War II, this sharashka designed both the Tupolev Tu-2 bomber and the Petlyakov Pe-2 dive bomber. The group was moved several times during the war, the first time to avoid capture by advancing German forces. Korolev was moved in 1942 to the sharashka of Kazan OKB-16 under Glushko. Korolev and Glushko designed the RD-1 kHz auxiliary rocket motor tested in an unsuccessful fast-climb Lavochkin La-7R. Korolev was isolated from his family until 27 June 1944 when he — along with Tupolev, Glushko and others — was finally discharged by special government decree, although the charges against him were not dropped until 1957.

Korolev rarely talked about his experience in the Gulag, and lived under constant fear of being executed for the military secrets he possessed. He was deeply affected by his time in the camp, becoming reserved and cautious as a result. He later learned that Glushko was one of his accusers, and this was likely the cause of the lifelong animosity between the two men. The design bureau was handed over from NKVD control to the government's aviation industry commission. Korolev continued working with the bureau for another year, serving as deputy designer under Glushko and studying various rocket designs.