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For Roth, earnings are always taxed when you withdraw them but contributions aren't. In this case he stated he did not withdraw earnings for 2015-2017 only excess contributions. So while he will have accrued penalties as previously described. I don't see something that would trigger more taxable income for those years as that is money that has already been taxed. Exception would be for his 2018 contribution when he caught the entire issue and he withdrew it AND the contributions prior to filing time.  Would a 2018 amendment be all that is needed to address the taxable earnings and penalty? That is assuming you can indeed file a 5329 by itself couldn't he do that for 2015, 2016, 2017.  What am I missing?