At this point you need to get a tax attorney and you will have to file an innocent spouse form with the IRS (Form 8857) disclaiming and proving no knowledge regarding the tax matters. You are eligible for relief if you filed a joint return on which there was an understatement of tax due to an erroneous item relating to your spouse; if you didn't know, and had no reason to know, about the understatement when you signed the return; if looking at all the facts and circumstances, it would be unfair to make you pay the tax, and; if you apply for relief under this provision within two years after the IRS begins trying to collect the tax from you.
If you meet all these requirements, then you don't have to pay the portion of tax that relates to this erroneous item.
This is available while still married. Innocent spouse relief may be available even if you're still married to, and living with, the spouse who should have reported additional tax. If you have assets of your own and want to protect them from collection by the IRS, these rules determine whether you can be held liable.
Lack of knowledge is the biggest factor here. If you only knew (or had reason to know) about part of the understatement of tax, you're only stuck for that part. If you had reason to believe your spouse was cheating to the extent of a few hundred dollars and it turned out to be many thousands, you should only have to pay the smaller amount. Thus, now you have knowledge you must report this to the IRS. However, since this just occurred you may indeed remain held liable still.
You need to sit with a local tax attorney immediately to discuss your options, such as filing separate tax returns immediately.
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