After you file

Sounds like you did fail to report all the income ... just because you didn't receive the tax forms you still had to report the income. If you believe all the income should have been on a W-2 not a 1099 then that is something you can argue. Or if you have expenses against that income you can amend the return and add the Sch C with expenses. What worries me the most is that you had pay stubs with withholding that the employer didn't remit to the IRS.   You may want to get an attorney that deals in employment law as you may have action for a lawsuit.   It may be best to get some professional help with this notice since there are a lot of moving parts ....

If you purchased Audit Defense for your tax return, call Tax Resources, Inc. at (877)-829-9695, or report your notice on their web site at http://intuit.taxaudit.com/. Do not contact the IRS. Let Tax Resources contact them for you.

This is the membership email you should have gotten: https://ttlc.intuit.com/questions/1901569-when-will-i-get-my-audit-defense-membership-kit

Also read the member agreement at this website -https://turbotax.intuit.com/corp/auditdefense.jsp

If you did not purchase Audit Defense:

TurboTax has a special phone number for help with IRS tax letters, which will be easier than going through regular Customer Support.   At the page below, click on the blue button that says "Get Help from TurboTax Support".  Then it will ask you what tax year is your letter.  Then it will ask you what the letter concerns. Then it will show you the phone number during posted business hours.

https://support.turbotax.intuit.com/irs-notice/audit-support/