diff --git a/data-machine.php b/data-machine.php
index fc9167ce..202085c7 100644
--- a/data-machine.php
+++ b/data-machine.php
@@ -243,6 +243,20 @@ function () {
 		new \DataMachine\Abilities\Handler\TestHandlerAbility();
 	} );
 
+	// Deferred scaffold: during plugin activation the Abilities API is unavailable
+	// because init fires before the plugin file is included. A transient signals that
+	// the scaffold needs to run on the first normal request where abilities are ready.
+	add_action(
+		'init',
+		function () {
+			if ( get_transient( 'datamachine_needs_scaffold' ) ) {
+				delete_transient( 'datamachine_needs_scaffold' );
+				datamachine_ensure_default_memory_files();
+			}
+		},
+		20 // After ability registration (priority 10).
+	);
+
 	// Clean up identity index rows when posts are permanently deleted.
 	add_action(
 		'before_delete_post',
@@ -543,7 +557,13 @@ function datamachine_activate_for_site() {
 	\DataMachine\Core\Database\Chat\Chat::ensure_agent_id_column();
 
 	// Ensure default agent memory files exist.
-	datamachine_ensure_default_memory_files();
+	// During activation the Abilities API is unavailable (init already fired before
+	// the plugin was included via plugin_sandbox_scrape, so our init callback that
+	// registers abilities never ran). Set a transient so the scaffold runs on the
+	// first normal request where the full hook sequence fires in order.
+	if ( ! datamachine_ensure_default_memory_files() ) {
+		set_transient( 'datamachine_needs_scaffold', 1, HOUR_IN_SECONDS );
+	}
 
 	// Run layered architecture migration (idempotent).
 	datamachine_migrate_to_layered_architecture();
diff --git a/inc/migrations.php b/inc/migrations.php
index 3467b6a4..17bb3039 100644
--- a/inc/migrations.php
+++ b/inc/migrations.php
@@ -1078,12 +1078,17 @@ function datamachine_copy_directory_recursive( string $source_dir, string $targe
  * (via DirectoryManager::ensure_agent_files()). Existing files are never
  * overwritten — only missing files are recreated from scaffold defaults.
  *
+ * Returns false when the Abilities API is unavailable (e.g. during plugin
+ * activation where init callbacks haven't fired), so the caller can defer.
+ *
  * @since 0.30.0
+ *
+ * @return bool True if scaffold ran, false if abilities were unavailable.
  */
-function datamachine_ensure_default_memory_files() {
+function datamachine_ensure_default_memory_files(): bool {
 	$ability = \DataMachine\Abilities\File\ScaffoldAbilities::get_ability();
 	if ( ! $ability ) {
-		return;
+		return false;
 	}
 
 	$default_user_id = \DataMachine\Core\FilesRepository\DirectoryManager::get_default_agent_user_id();
@@ -1093,6 +1098,8 @@ function datamachine_ensure_default_memory_files() {
 
 	// Scaffold default context memory files (contexts/{context}.md).
 	datamachine_ensure_default_context_files( $default_user_id );
+
+	return true;
 }
 
 /**