What happened to religion during the communist rule?

It never disappeared. In Russia it remained tolerated by the Communist Party because the Russian Orthodox Church had (and still has) an age-old policy of subjecting itself to the State and its rulers and never become openly critical of the rulers' policies and actions. The Communists also realized that outlawing religion would only drive it underground and make it much harder to control or manage. Only Party members would stay away from Church services, because active membership would disqualify them for advancement within the Party.

Other Communist countries showed the same picture. Poland's Communist Party did not even dare to actively discourage its own members from being regular church goers. In Poland, the Roman Catholic Church in time became the most powerful and active anti-Communist force.