The word "accused" generally connotes criminal activity. There is a distinct field of criminal tax and if you have been visited by an IRS Special Agent that means you are being investigated for criminal tax issues. You can tell that she is a Special Agent because she carries a gun. And they usually do not travel alone, they have another Special Agent partner to take notes on everything you say. In purely civil (monetary only) matters you will be dealing with a Revenue Agent. Some of them are quite officious and keep referring to their "badge number" but rest assured, they are not allowed to carry guns. Their badge number is not like a law enforcement officer you would commonly think of as a gruff LAPD officer approaching you with a weapon drawn. Revenue agents typically come from a purely accounting background and they are there to make sure the numbers all line up.

In the majority of all cases, if you have been contacted by the IRS it is purely a civil issue and the only penalties would be monetary. But each case is unique and depends on the facts. This is just a general discussion of procedural matters. If we are simply talking about a civil issue then the IRS is bifurcated into Examination and Appeals. If you received a Notice of Review that means your return(s) were selected based on a computer algorithm and a pair of human eyes at the IRS are going to review it. This is typically when one would engage a tax professional (CPA, tax attorney, or enrolled agent) to represent their interests before the IRS, because once a pair of eyes are on a return then generally the next step is you will receive a Notice of Examination and that is when the audit begins. The revenue agent will begin the audit and issue Information Document Requests (IDRs) to begin the audit. The benefit of having a tax professional represent you before the IRS is that they know "the code" and the administrative process and can help the agent understand what is happening on your return. Without an experienced tax professional who knows tax law, the only option is to talk to a revenue agent with normal everyday language, and they are much more comfortable speaking tax jargon to other people who also speak tax jargon.

It is strategically best for a Taxpayer to resolve the audit in Examination, otherwise the revenue agent will close out the audit and assess penalties. At this point you will be dealing with IRS Appeals to try and resolve the matter. There is also Fast Track Mediation before Appeals and Post Appeals Mediation after Appeals, in certain instances, but typically Appeals will be your last bite at the administrative apple to resolve the audit as favorably as possible before having to go through litigation. IRS Appeals is an independent review of the revenue agent's findings - the Appeals Officer is not allowed to have ex parte communication with the agent. However you can present more information in Appeals. If you have not resolved the matter in Appeals and they close out the audit, then you will have to file suit in Tax Court or the federal district court, depending on certain factors. If it is a criminal tax issue then the IRS Special Agent will investigate, and there will be a SAC (Special Agent in Charge) meeting which is the last chance to avoid the possibility of being a criminal defendant once the matter is turned over to DOJ Criminal Tax for potential prosecution. DOJ Tax might reject the case, or send it back to the Special Agent to do more investigation and build a stronger case. Otherwise it is time for the grand jury.

The most important thing to keep in mind, especially as an individual not represented by a tax professional, or the owner/shareholder/CFO etc. of a small to mid size business, is that you catch more bees with honey than vinegar. Nobody likes when the IRS appears on their doorstep. However it is your own advantage to be professional, stick to the facts, apply the law, and get the audit over as quickly as possible. Being rude and unprofessional does not help you achieve that goal.

Seeing as this is an introductory there is not much more to add because the nuances swallow the general rules, because every situation is different. I cannot overstate the important of having a qualified tax professional represent you before the IRS. If you try to "cheap it" and represent yourself in the audit, you will blow through Examination and IRS Appeals losing all attempts to amicably and favorably resolve your issue. Also the subsequent litigation, should you be able to afford to fight it out in Tax Court or federal district court (depending on a number of factors which court you would be in) will be based on the facts presented before Examination and Appeals, which makes it absolutely essential to put everything, framed properly, in front of the IRS before it is too late.