/*
Plugin Name: Name of Plugin
Plugin URI: Link to plugin information
Description: Plugin Description
[...]
Network: Optional. Specify "Network: true" to require that a plugin is activated
       across all sites in an installation. This will prevent a plugin from being
       activated on a single site when Multisite is enabled.
*/

add_filter( 'all_plugins', 'wpse257256_hide_my_plugin' );
function wpse257256_hide_my_plugin( $plugins ) {
    if ( is_multisite() && ! is_network_admin() ) {
        unset( $plugins['my-plugin-name/my-plugin-file.php'] );
    }
    return $plugins;
}

register_activation_hook( __FILE__,  function () {
    if ( is_multisite() && ! strpos( $_SERVER['REQUEST_URI'], 'wp-admin/network/plugins.php' ) ) {
        die ( __( '<script>alert("Activate this plugin only from the NETWORK DASHBOARD.");</script>') );
    }
    // ...............
});