You can file all pending Returns with tax payable along with applicable late fees (as it's limited to 500/Nil per month as the case may be up to 30th September, 2020) and interest, if any.
Otherwise, officer can issue show cause notice for non filing of return or also can do best judgement assessment, if required and cancel GST registration on it own.
The return needs to be filed for Mar April, May and June. Therefore late fees of would₹500/month would be payable over and above a Tax liability along with interest.