You can clearly see the way WordPress loads plugins if you inspect the source code of the file wp-settings.php.
The function wp_get_active_and_valid_plugins() loads plugins for individual sites in the network and for non-Multi-Site installations, while wp_get_active_network_plugins() loads network activated plugins when Multi-Site is enabled.
The former more or less just calls get_option() to get the active_plugins option from the wp_options database table, while the latter uses get_site_option() which is the network-wide version of get_option(). The option which has the network enabled plugins is called active_sitewide_plugins.