Separate Business returns or a Schedule C in your personal return for self employment/sole proprietor? You should go to a local accountant to get that caught up. It may not be a do it yourself situation.
If your business entity is a Partnership or multi-member LLC (Form 10165) or an incorporated LLC filing as a S Corp (Form 1120S) or a C Corp (Form 1120) then you definitely need to use the services of a paid tax professional in your local area that is familiar with these types of business tax returns and the implications of not filing for the past three years. This is not something that you can do with do-it-yourself tax preparation software like TurboTax.