diff --git a/features/checksum-plugin.feature b/features/checksum-plugin.feature
index ea6cb19e..41776542 100644
--- a/features/checksum-plugin.feature
+++ b/features/checksum-plugin.feature
@@ -204,3 +204,37 @@ 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
+      """
diff --git a/src/Checksum_Plugin_Command.php b/src/Checksum_Plugin_Command.php
index 64509d42..dcb46af4 100644
--- a/src/Checksum_Plugin_Command.php
+++ b/src/Checksum_Plugin_Command.php
@@ -107,6 +107,12 @@ 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;
@@ -222,24 +228,87 @@ private function get_plugin_version( $path ) {
 		}
 
 		if ( ! array_key_exists( $path, $this->plugins_data ) ) {
-			return false;
+			// Try to detect version from any PHP file in the plugin directory
+			return $this->detect_version_from_directory( dirname( $path ) );
 		}
 
 		return $this->plugins_data[ $path ]['Version'];
 	}
 
+	/**
+	 * Attempts to detect plugin version from any PHP file in the plugin directory.
+	 *
+	 * This is used as a fallback when the main plugin file is missing or has no valid headers.
+	 *
+	 * @param string $plugin_dir Plugin directory name (relative to WP_PLUGIN_DIR).
+	 *
+	 * @return string|false Detected version, or false if not found.
+	 */
+	private function detect_version_from_directory( $plugin_dir ) {
+		$plugin_path = WP_PLUGIN_DIR . '/' . $plugin_dir;
+
+		// If it's not a directory (single-file plugin), we can't detect version
+		if ( ! is_dir( $plugin_path ) ) {
+			return false;
+		}
+
+		// Try scanning PHP files for Version header using WordPress's get_file_data()
+		$files = glob( $plugin_path . '/*.php' );
+		if ( is_array( $files ) && ! empty( $files ) ) {
+			foreach ( $files as $file ) {
+				if ( is_readable( $file ) ) {
+					$file_data = get_file_data(
+						$file,
+						array( 'Version' => 'Version' )
+					);
+					if ( ! empty( $file_data['Version'] ) ) {
+						return $file_data['Version'];
+					}
+				}
+			}
+		}
+		// If glob() failed (returns false), version will just not be detected from PHP files
+
+		return false;
+	}
+
 	/**
 	 * 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 );
 		}
 
-		return $names;
+		// Also scan the filesystem for plugin directories
+		$plugin_dir = WP_PLUGIN_DIR;
+		if ( is_dir( $plugin_dir ) && is_readable( $plugin_dir ) ) {
+			$dirs = @scandir( $plugin_dir ); // phpcs:ignore WordPress.PHP.NoSilencedErrors.Discouraged
+			if ( false !== $dirs ) {
+				foreach ( $dirs as $dir ) {
+					// Skip special directories and files
+					if ( '.' === $dir || '..' === $dir ) {
+						continue;
+					}
+
+					$full_path = $plugin_dir . '/' . $dir;
+					// Only include real directories, not symlinks or files
+					if ( is_dir( $full_path ) && ! is_link( $full_path ) && ! in_array( $dir, $names, true ) ) {
+						$names[] = $dir;
+					}
+				}
+			}
+		}
+
+		return array_unique( $names );
 	}
 
 	/**
diff --git a/src/WP_CLI/Fetchers/UnfilteredPlugin.php b/src/WP_CLI/Fetchers/UnfilteredPlugin.php
index 2cac264e..83c18d38 100644
--- a/src/WP_CLI/Fetchers/UnfilteredPlugin.php
+++ b/src/WP_CLI/Fetchers/UnfilteredPlugin.php
@@ -25,6 +25,7 @@ class UnfilteredPlugin extends Base {
 	 * @return object|false
 	 */
 	public function get( $name ) {
+		// First, check plugins detected by get_plugins()
 		foreach ( get_plugins() as $file => $_ ) {
 			if ( "{$name}.php" === $file ||
 				( $name && $file === $name ) ||
@@ -33,6 +34,16 @@ 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;
+		if ( is_dir( $plugin_dir ) ) {
+			// 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;
 	}
 }