After you file

yes there can be substantial penalties for failure to file and failure to pay. get your new CPA involved in this ASAP.  they should be using their best effort to correct the situation and possibly contacting the IRS in order to see what can be done with regard to potential penalties.   If the previous accountant was in fact a CPA, you should contact your state's professional CPA society. his license could be revoked and you might be helping others by doing this.  you may also want to contact a lawyer especially if there are penalties.