A normal audit checks the homepage. A deep audit checks up to 50 pages discovered from your sitemap.xml and aggregates the results into a single weighted-mean site score (homepage counts double).
To run one: open the site detail page and click Deep audit. The parent audit row is created immediately and child audits run in the background; the result page auto-refreshes every 6 seconds so you can watch pages flip green. When all children finish, the aggregator writes per-category averages onto the parent and fires the audit-complete email/Slack alert.
Deep audits are Pro-only because they cost roughly 50x a single audit in compute time. The button shows "Pro feature" with an Upgrade CTA on free/Solo accounts.