‘I hired a contractor to build an addition to our home that included new plumbing. His subcontractor installed a drain into the storm water system thinking it was a sewer pipe. The city gave us a plumbing permit. The city is now coming after us for an illegal drain. What can we do?’

Fix it.

The city will insist that the drain be repaired properly, and they probably have some pretty serious powers to enforce that. The fact that they may have signed off on the permit is irrelevant; even if it’s their fault, you still have an obligation to maintain your property up to code.

I would suggest contacting your contractor and calmly letting him know that this needs to be done. Assuming his sub is at all professional, he should make the change at no charge (assuming the original contract was a flat bid).