diff --git a/features/checksum-plugin.feature b/features/checksum-plugin.feature
index 41131c35..98920c6f 100644
--- a/features/checksum-plugin.feature
+++ b/features/checksum-plugin.feature
@@ -183,6 +183,44 @@ Feature: Validate checksums for WordPress plugins
       Verified 1 of 1 plugins.
       """
 
+  Scenario: Verifies plugin directory when main file is missing
+    Given a WP install
+
+    When I run `wp plugin install duplicate-post --version=3.2.1`
+    Then STDOUT should not be empty
+    And STDERR should be empty
+
+    When I run `mv wp-content/plugins/duplicate-post/duplicate-post.php wp-content/plugins/duplicate-post/duplicate-post.php.renamed`
+    Then STDERR should be empty
+
+    When I try `wp plugin verify-checksums duplicate-post --version=3.2.1 --format=json`
+    Then STDOUT should contain:
+      """
+      "plugin_name":"duplicate-post","file":"duplicate-post.php.renamed","message":"File was added"
+      """
+    And STDERR should contain:
+      """
+      Warning: Plugin duplicate-post main file is missing: duplicate-post/duplicate-post.php
+      """
+    And STDERR should contain:
+      """
+      Error: No plugins verified (1 failed).
+      """
+
+    When I try `wp plugin verify-checksums --all --format=json`
+    Then STDOUT should contain:
+      """
+      "plugin_name":"duplicate-post"
+      """
+    And STDERR should contain:
+      """
+      Warning: Plugin duplicate-post main file is missing: duplicate-post/duplicate-post.php
+      """
+    And STDERR should contain:
+      """
+      Warning: Could not determine the version of plugin duplicate-post from its files.
+      """
+
   Scenario: Verify must-use plugin that is a standard plugin moved to mu-plugins
     Given a WP install
 
diff --git a/src/Checksum_Plugin_Command.php b/src/Checksum_Plugin_Command.php
index 32a2f119..cf3f38f2 100644
--- a/src/Checksum_Plugin_Command.php
+++ b/src/Checksum_Plugin_Command.php
@@ -26,6 +26,13 @@ class Checksum_Plugin_Command extends Checksum_Base_Command {
 	 */
 	private $errors = array();
 
+	/**
+	 * Whether to skip TLS certificate verification for remote requests.
+	 *
+	 * @var bool
+	 */
+	private $insecure = false;
+
 	/**
 	 * Verifies plugin files against WordPress.org's checksums.
 	 *
@@ -77,13 +84,14 @@ class Checksum_Plugin_Command extends Checksum_Base_Command {
 	 */
 	public function __invoke( $args, $assoc_args ) {
 
-		$fetcher    = new Fetchers\UnfilteredPlugin();
-		$all        = Utils\get_flag_value( $assoc_args, 'all', false );
-		$strict     = Utils\get_flag_value( $assoc_args, 'strict', false );
-		$insecure   = Utils\get_flag_value( $assoc_args, 'insecure', false );
-		$exclude_mu = Utils\get_flag_value( $assoc_args, 'exclude-mu-plugins', false );
-		$plugins    = $fetcher->get_many( $all ? $this->get_all_plugin_names() : $args );
-		$mu_plugins = ! $exclude_mu ? array_merge( get_mu_plugins(), get_plugins( '/../' . basename( WPMU_PLUGIN_DIR ) ) ) : [];
+		$fetcher        = new Fetchers\UnfilteredPlugin();
+		$all            = Utils\get_flag_value( $assoc_args, 'all', false );
+		$strict         = Utils\get_flag_value( $assoc_args, 'strict', false );
+		$this->insecure = Utils\get_flag_value( $assoc_args, 'insecure', false );
+		$insecure       = $this->insecure;
+		$exclude_mu     = Utils\get_flag_value( $assoc_args, 'exclude-mu-plugins', false );
+		$plugins        = $fetcher->get_many( $all ? $this->get_all_plugin_names() : $args );
+		$mu_plugins     = ! $exclude_mu ? array_merge( get_mu_plugins(), get_plugins( '/../' . basename( WPMU_PLUGIN_DIR ) ) ) : [];
 
 		/**
 		 * @var string $exclude
@@ -112,6 +120,12 @@ public function __invoke( $args, $assoc_args ) {
 				continue;
 			}
 
+			// Check if the main plugin file exists
+			$main_file_path = WP_PLUGIN_DIR . '/' . $plugin->file;
+			if ( ! file_exists( $main_file_path ) ) {
+				WP_CLI::warning( "Plugin {$plugin->name} main file is missing: {$plugin->file}" );
+			}
+
 			if ( false === $version ) {
 				WP_CLI::warning( "Could not retrieve the version for plugin {$plugin->name}, skipping." );
 				++$skips;
@@ -251,23 +265,75 @@ private function get_plugin_version( $path ) {
 		}
 
 		if ( ! array_key_exists( $path, $this->plugins_data ) ) {
-			return false;
+			return $this->fetch_version_from_wp_org( dirname( $path ) );
 		}
 
 		return $this->plugins_data[ $path ]['Version'];
 	}
 
+	/**
+	 * Fetches the current stable plugin version from WordPress.org as a fallback.
+	 *
+	 * Used when the plugin version cannot be determined locally (e.g. main file missing).
+	 * Logs a warning to indicate that the version is being assumed.
+	 *
+	 * @param string $plugin_slug Plugin slug.
+	 *
+	 * @return string|false Stable version from WordPress.org, or false on failure.
+	 */
+	private function fetch_version_from_wp_org( $plugin_slug ) {
+		$wp_org_api = new WpOrgApi( [ 'insecure' => $this->insecure ] );
+
+		try {
+			$plugin_data = $wp_org_api->get_plugin_info( $plugin_slug );
+		} catch ( Exception $exception ) {
+			return false;
+		}
+
+		if ( ! is_array( $plugin_data ) || empty( $plugin_data['version'] ) ) {
+			return false;
+		}
+
+		$version = $plugin_data['version'];
+		WP_CLI::warning( "Could not determine the version of plugin {$plugin_slug} from its files. Assuming the current stable version ({$version}) from WordPress.org." );
+
+		return $version;
+	}
+
 	/**
 	 * Gets the names of all installed plugins.
 	 *
+	 * Includes both plugins detected by get_plugins() and plugin directories
+	 * that exist on the filesystem but may not have valid headers.
+	 *
 	 * @return array<string> Names of all installed plugins.
 	 */
 	private function get_all_plugin_names() {
 		$names = array();
+
+		// Get plugins from get_plugins() (those with valid headers)
 		foreach ( get_plugins() as $file => $details ) {
 			$names[] = Utils\get_plugin_name( $file );
 		}
 
+		// Also scan the filesystem for plugin directories
+		$plugin_dir = WP_PLUGIN_DIR;
+		if ( is_dir( $plugin_dir ) && is_readable( $plugin_dir ) ) {
+			try {
+				foreach ( new DirectoryIterator( $plugin_dir ) as $fileinfo ) {
+					if ( $fileinfo->isDot() || ! $fileinfo->isDir() || $fileinfo->isLink() ) {
+						continue;
+					}
+					$dir = $fileinfo->getFilename();
+					if ( ! in_array( $dir, $names, true ) ) {
+						$names[] = $dir;
+					}
+				}
+			} catch ( UnexpectedValueException $e ) {
+				WP_CLI::warning( "Could not scan plugin directory '{$plugin_dir}': " . $e->getMessage() );
+			}
+		}
+
 		return $names;
 	}
 
diff --git a/src/WP_CLI/Fetchers/UnfilteredPlugin.php b/src/WP_CLI/Fetchers/UnfilteredPlugin.php
index 4076178b..152cbf35 100644
--- a/src/WP_CLI/Fetchers/UnfilteredPlugin.php
+++ b/src/WP_CLI/Fetchers/UnfilteredPlugin.php
@@ -28,6 +28,7 @@ class UnfilteredPlugin extends Base {
 	public function get( $name ) {
 		$name = (string) $name;
 
+		// First, check plugins detected by get_plugins()
 		foreach ( get_plugins() as $file => $_ ) {
 			if ( "{$name}.php" === $file ||
 				( $name && $file === $name ) ||
@@ -36,6 +37,27 @@ public function get( $name ) {
 			}
 		}
 
+		// If not found, check if a directory with this name exists
+		// This handles cases where the main plugin file is missing
+		$plugin_dir = WP_PLUGIN_DIR . '/' . $name;
+
+		// Resolve real paths to protect against path traversal and symlinks.
+		$wp_plugin_dir_real = realpath( WP_PLUGIN_DIR );
+		$plugin_dir_real    = realpath( $plugin_dir );
+
+		if ( false !== $wp_plugin_dir_real
+			&& false !== $plugin_dir_real
+			&& is_dir( $plugin_dir_real )
+			&& ! is_link( $plugin_dir_real )
+			&& ( $plugin_dir_real === $wp_plugin_dir_real
+				|| 0 === strpos( $plugin_dir_real, $wp_plugin_dir_real . DIRECTORY_SEPARATOR ) )
+		) {
+			// Use the conventional main file name, even if it doesn't exist
+			// The checksum verification will handle missing files appropriately
+			$file = $name . '/' . $name . '.php';
+			return (object) compact( 'name', 'file' );
+		}
+
 		return false;
 	}
 }