The gradual deletion is performed by the Timer Job Definition called Gradual Site Delete.
In few words:
The site reference is being deleted from SiteMap and Sites tables of configuration and content databases and added into the SiteDeletion table. The Site collection is unavalaible for users. But sub-sites still exist in the Webs table of content database. This behavior can cause some issues for third-party tools which read these tables.
The Gradual Site Delete Timer Job definition is scheduled to be runnin one time a day. It can be started manually from Central Administration -> Monitoring -> Review job definitions -> Gradual Site Delete.
Here you can edit the timer job or run the job immediately
Refer the following article for more detailed information about the Gradual Site Delete timer job definition.
To delete the site collection completely use the following Powershell command: