MassProtect provides a link to a modal which allows the user to list pages to be protected. Protection options include edit, move, upload, and create with various levels: unset, none ("Allow all users"), autoconfirmed ("Block new and unregistered users"), and sysop ("Administrators and Content Moderators only").
In order to protect multiple pages, add the page names (not page URLs) each on a new line (including their namespace if necessary) and proceed to protect them. The script will stop when it reaches an empty line.
By default, the script will do one page per second. If you'd like to modify that, add the config window.massProtectDelay before importing the script with your own number (in milliseconds) instead.
The option to use the Mass Protect script will appear under your "My Tools" list (the toolbar at the bottom of your screen).