You are confusing the issues here:

• The assets were sold at the entity level.  Any gain or loss is determined at the entity level.  The shareholder basis has nothing to do with this transaction.
• Based on your additional facts, since the intangible was purchased previously, you are able to use the $200,000 basis when determining your gain.
• Based on bullet 2, the split in the gain noted previously still applies; so this addresses your $2 mil.
• If you still have assets on the books after the transaction, then someone needs to determine what happens next; will the S corp remain and operate with those remaining assets or will the S corp be closed down?
• Depending on the decision to bullet 4, that will require an additional set of adjustments as it is not part of your initial question regarding the sale transaction.
• The piece that you are also probably missing is that the gain passes through to the shareholder, the shareholder pays tax, the shareholder should receive a distribution (current or liquidating depends on the response to bullet 4) to cover any tax AND the shareholder basis is increased by the gain passed through on the transaction.