The money paid will go to Ireland. Ireland allowed Apple to structure its tax affairs in a way that reduced their tax bill which is a great incentive to maintain a presence there.

The EU has now determined this was an illegal tax benefit provided by Ireland, so Ireland must now collect the tax as if it had done so at the time. There is no penalty but interest must be paid.

This is not your normal run of the mill tax avoidance case (or a fraud as you've mentioned) although it appears to look the same. This was Apple benefiting from decisions taken by Ireland that Ireland should not have made.