The next step is to figure out what the hacker was after. Was it consumer or employee PII?
Was it your proprietary shopping cart script? Check your server logs for any modified, uploaded or otherwise suspicious file activities.
Once you've assessed the situation, reinstall your OS--preferably from a secure, trusted site or disc. After the fresh reinstallation, use the latest backup you have to restore your site--but make sure that the backup is clean and free of compromised content. Change your passwords, and if your site was offline, take the steps to get it back online and work on getting the engines to start indexing it again.