I recently ran into an issue where one of our Site Collections got mysteriously deleted. I’m still figuring out the logs to see how it happened, but I came across a quick and easy PowerShell command to restore the Site Collection when I couldn’t find it in any of the recycle bins.
Get-SPDeletedSite | Restore-SPDeletedSite
This command will give you a list of recently deleted site collections and then prompt you to restore each of them individually.