By default, deactivating Security Ninja does not delete settings, scans, logs, or cached files. That is the safe choice when you are debugging a conflict and want the same configuration back.

Scheduled jobs still stop while the plugin is inactive. They start again when you reactivate.

The switch

On Security Ninja → Tools, use Remove settings when deactivating.

Leave it off (default) to keep settings, scan results, logs, and cached files.

Turn it on only when you want a clean deactivation: settings and stored scan and log data are removed. Your license activation is kept, so you can reactivate without entering the key again.

This is one central switch for every module. It is available in Free and Pro (Security Ninja 5.303 and later).

Deactivate vs delete

Deactivate, switch off: Settings and data stay. Cron jobs stop until you reactivate.
Deactivate, switch on: Settings, scans, logs, module tables, cached files, and related user metadata are removed. License state stays so you can turn the plugin back on.
Delete the plugin (uninstall): Always clears module tables, settings, cached files, and related user metadata. The saved license state is removed too.

Firewall and other protections do not come back automatically after a wipe. Configure them again after you reinstall.

If you only need to get back into wp-admin after a lockout, deactivate from the filesystem instead of wiping data. See How to deactivate the plugin.