The deportations the Soviet Union carried out were before the miktiopolis project came to be, thus they would have happened as they did in our history.

Crimea did become an independent country, the Republic of Crimea, and then joined the Russian federation.
It began with president Viktor Yanukovich signing an agreement for the initiation of a miktiopolis project city on the Crimean peninsula. It was meant to create better ties with the EU and attract more funding that would stabilize the country. However, the president made a last minute decision that the city would not be located on the peninsula, but by the Dnepr river in Poltavska region. This triggered a protest by the people of Crimea, who were dissatisfied with this decision. The country had not payed much mind to the peninsula and the eastern areas for years, barely giving them any funding to fix their roads and develop any form of business. To calm down the crowds the president assured that they should not worry, because the second shareholder of the miktiopolis would be Russia. This made the protesters go relatively quiet, because the vast majority of them were Russians, however, this triggered an even bigger wave of anti-Russian protests, which lead to an anti-Yanukovich protests that accused Yanukovich for turning his back on the EU and gazing towards Russia (which was in fact true). The protests continued for months and lead to Yanukovich fleeing his country and vanishing from the public's eye. Ukrane's new president, Aleskandr Turchynov, forbid any language, other than Ukrainian, to be considered an official language. No sign could be written in a language other than Ukrainian, people could not do any business in another language and children would only be taught one official language - Ukrainian, whilst everything else was foreign. This caused an uproar in Crimea, Odesa, Dunetsk and Lugansk, where the majority of the population was Russian and they wished to remain as such. After a protest that took down the local government, the people of Crimea organized a referendum, which deemed that the people wished for independence. Former military officers and those from the military forces in Crimea organized the resistance against the Ukrainian forces. The UN General Assembly declared that the referendum was valid, despite the USA stating that it was invalid. After becoming independent, the Republic of Crimea asked to join the Russian Federation and was accepted.