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Theory time: They weren't experimenting a bomb during the Anastasia development, but they were creating a person who can destroy a nation all by himself. And which perfect candidate with resources no one can have? Zhenya with his family backing. Zhenya with his psychopathic behavior popping up when he was young. Everything really points to Zhenya.
They "failed" because there is probably something Zhenya did like disobeying orders from the nation so the people in charge died as crowd control. So the Bogdanov people are the only ones alive to keep the mystery of Anastasia alive. Zhenya was the bomb they were looking for all along.