Just file it. You may end up underpaying the penalties and interest, if you do they'll send you a statement for the difference.

The important thing is to comply with your obligations and get any underpayment down to a small amount ASAP.

In my case I got a little fixated on exactly computing the penalties plus interest which delayed resolving it. While researching it I found a court case where the IRS was asking the court for permission to approximate the interest because it was too complicated to compute. 0_o. At that point I gave up trying to compute it myself, but immediately after they sent me another notice with updated values and that was enough to disambiguate the two competing readings of the tax code and I was able to pay it exactly. :P

Almost two decades later I know better-- just put in a reasonable effort and let the IRS worry about it.

You file it and the IRS sends you a piece of mail that asks you to deal with it.

I recently did it for a 13 yo company missing many years of taxes and it wasn't a huge deal.