diff --git a/MCPForUnity/Editor/MenuItems/MCPForUnityMenu.cs b/MCPForUnity/Editor/MenuItems/MCPForUnityMenu.cs
index 32fde720..10f05248 100644
--- a/MCPForUnity/Editor/MenuItems/MCPForUnityMenu.cs
+++ b/MCPForUnity/Editor/MenuItems/MCPForUnityMenu.cs
@@ -5,42 +5,25 @@
 
 namespace MCPForUnity.Editor.MenuItems
 {
-    /// <summary>
-    /// Centralized menu items for MCP For Unity
-    /// </summary>
     public static class MCPForUnityMenu
     {
-        // ========================================
-        // Main Menu Items
-        // ========================================
-
-        /// <summary>
-        /// Show the Setup Window
-        /// </summary>
         [MenuItem("Window/MCP For Unity/Setup Window", priority = 1)]
         public static void ShowSetupWindow()
         {
             SetupWindowService.ShowSetupWindow();
         }
 
-        /// <summary>
-        /// Toggle the main MCP For Unity window
-        /// </summary>
         [MenuItem("Window/MCP For Unity/Toggle MCP Window %#m", priority = 2)]
         public static void ToggleMCPWindow()
         {
-            if (EditorWindow.HasOpenInstances<MCPForUnityEditorWindow>())
+            if (MCPForUnityEditorWindow.HasAnyOpenWindow())
             {
-                foreach (var window in UnityEngine.Resources.FindObjectsOfTypeAll<MCPForUnityEditorWindow>())
-                {
-                    window.Close();
-                }
+                MCPForUnityEditorWindow.CloseAllOpenWindows();
             }
             else
             {
                 MCPForUnityEditorWindow.ShowWindow();
             }
         }
-
     }
 }
diff --git a/MCPForUnity/Editor/Setup/SetupWindowService.cs b/MCPForUnity/Editor/Setup/SetupWindowService.cs
index 2045ba45..99a037a2 100644
--- a/MCPForUnity/Editor/Setup/SetupWindowService.cs
+++ b/MCPForUnity/Editor/Setup/SetupWindowService.cs
@@ -18,7 +18,11 @@ public static class SetupWindowService
     {
         private const string SETUP_COMPLETED_KEY = EditorPrefKeys.SetupCompleted;
         private const string SETUP_DISMISSED_KEY = EditorPrefKeys.SetupDismissed;
-        private static bool _hasCheckedThisSession = false;
+
+        // Use SessionState to persist "checked this editor session" across domain reloads.
+        // SessionState survives assembly reloads within the same Editor session, which prevents
+        // the setup window from reappearing after code reloads / playmode transitions.
+        private const string SessionCheckedKey = "MCPForUnity.SetupWindowCheckedThisEditorSession";
 
         static SetupWindowService()
         {
@@ -35,10 +39,12 @@ static SetupWindowService()
         /// </summary>
         private static void CheckSetupNeeded()
         {
-            if (_hasCheckedThisSession)
+            // Ensure we only run once per Editor session (survives domain reloads).
+            // This avoids showing the setup dialog repeatedly when scripts recompile or Play mode toggles.
+            if (SessionState.GetBool(SessionCheckedKey, false))
                 return;
 
-            _hasCheckedThisSession = true;
+            SessionState.SetBool(SessionCheckedKey, true);
 
             try
             {
@@ -48,11 +54,16 @@ private static void CheckSetupNeeded()
                 bool userOverrodeHttpUrl = EditorPrefs.HasKey(EditorPrefKeys.HttpBaseUrl);
 
                 // In Asset Store builds with a remote default URL (and no user override), skip the local setup wizard.
-                if (!userOverrodeHttpUrl
+                if (
+                    !userOverrodeHttpUrl
                     && McpDistribution.Settings.skipSetupWindowWhenRemoteDefault
-                    && McpDistribution.Settings.IsRemoteDefault)
+                    && McpDistribution.Settings.IsRemoteDefault
+                )
                 {
-                    McpLog.Info("Skipping Setup Window because this distribution ships with a hosted MCP URL. Open Window/MCP For Unity/Setup Window if you want to configure a local runtime.", always: false);
+                    McpLog.Info(
+                        "Skipping Setup Window because this distribution ships with a hosted MCP URL. Open Window/MCP For Unity/Setup Window if you want to configure a local runtime.",
+                        always: false
+                    );
                     return;
                 }
 
@@ -66,7 +77,10 @@ private static void CheckSetupNeeded()
                 }
                 else
                 {
-                    McpLog.Info("Setup Window skipped - previously completed or dismissed", always: false);
+                    McpLog.Info(
+                        "Setup Window skipped - previously completed or dismissed",
+                        always: false
+                    );
                 }
             }
             catch (Exception ex)
@@ -108,6 +122,5 @@ public static void MarkSetupDismissed()
             EditorPrefs.SetBool(SETUP_DISMISSED_KEY, true);
             McpLog.Info("Setup marked as dismissed");
         }
-
     }
 }
diff --git a/MCPForUnity/Editor/Windows/MCPForUnityEditorWindow.cs b/MCPForUnity/Editor/Windows/MCPForUnityEditorWindow.cs
index 1dfada10..ccc47ca9 100644
--- a/MCPForUnity/Editor/Windows/MCPForUnityEditorWindow.cs
+++ b/MCPForUnity/Editor/Windows/MCPForUnityEditorWindow.cs
@@ -1,14 +1,14 @@
 using System;
 using System.Collections.Generic;
 using System.Threading.Tasks;
-using UnityEditor;
-using UnityEngine;
-using UnityEngine.UIElements;
 using MCPForUnity.Editor.Helpers;
 using MCPForUnity.Editor.Services;
-using MCPForUnity.Editor.Windows.Components.Settings;
-using MCPForUnity.Editor.Windows.Components.Connection;
 using MCPForUnity.Editor.Windows.Components.ClientConfig;
+using MCPForUnity.Editor.Windows.Components.Connection;
+using MCPForUnity.Editor.Windows.Components.Settings;
+using UnityEditor;
+using UnityEngine;
+using UnityEngine.UIElements;
 
 namespace MCPForUnity.Editor.Windows
 {
@@ -20,14 +20,47 @@ public class MCPForUnityEditorWindow : EditorWindow
         private McpClientConfigSection clientConfigSection;
 
         private static readonly HashSet<MCPForUnityEditorWindow> OpenWindows = new();
+        private bool guiCreated = false;
 
         public static void ShowWindow()
         {
             var window = GetWindow<MCPForUnityEditorWindow>("MCP For Unity");
             window.minSize = new Vector2(500, 600);
         }
+
+        // Helper to check and manage open windows from other classes
+        public static bool HasAnyOpenWindow()
+        {
+            return OpenWindows.Count > 0;
+        }
+
+        public static void CloseAllOpenWindows()
+        {
+            if (OpenWindows.Count == 0)
+                return;
+
+            // Copy to array to avoid modifying the collection while iterating
+            var arr = new MCPForUnityEditorWindow[OpenWindows.Count];
+            OpenWindows.CopyTo(arr);
+            foreach (var window in arr)
+            {
+                try
+                {
+                    window?.Close();
+                }
+                catch (Exception ex)
+                {
+                    McpLog.Warn($"Error closing MCP window: {ex.Message}");
+                }
+            }
+        }
+
         public void CreateGUI()
         {
+            // Guard against repeated CreateGUI calls (e.g., domain reloads)
+            if (guiCreated)
+                return;
+
             string basePath = AssetPathUtility.GetMcpPackageRootPath();
 
             // Load main window UXML
@@ -37,7 +70,9 @@ public void CreateGUI()
 
             if (visualTree == null)
             {
-                McpLog.Error($"Failed to load UXML at: {basePath}/Editor/Windows/MCPForUnityEditorWindow.uxml");
+                McpLog.Error(
+                    $"Failed to load UXML at: {basePath}/Editor/Windows/MCPForUnityEditorWindow.uxml"
+                );
                 return;
             }
 
@@ -78,8 +113,10 @@ public void CreateGUI()
                 var settingsRoot = settingsTree.Instantiate();
                 sectionsContainer.Add(settingsRoot);
                 settingsSection = new McpSettingsSection(settingsRoot);
-                settingsSection.OnGitUrlChanged += () => clientConfigSection?.UpdateManualConfiguration();
-                settingsSection.OnHttpServerCommandUpdateRequested += () => connectionSection?.UpdateHttpServerCommandDisplay();
+                settingsSection.OnGitUrlChanged += () =>
+                    clientConfigSection?.UpdateManualConfiguration();
+                settingsSection.OnHttpServerCommandUpdateRequested += () =>
+                    connectionSection?.UpdateHttpServerCommandDisplay();
             }
 
             // Load and initialize Connection section
@@ -91,7 +128,8 @@ public void CreateGUI()
                 var connectionRoot = connectionTree.Instantiate();
                 sectionsContainer.Add(connectionRoot);
                 connectionSection = new McpConnectionSection(connectionRoot);
-                connectionSection.OnManualConfigUpdateRequested += () => clientConfigSection?.UpdateManualConfiguration();
+                connectionSection.OnManualConfigUpdateRequested += () =>
+                    clientConfigSection?.UpdateManualConfiguration();
             }
 
             // Load and initialize Client Configuration section
@@ -105,6 +143,8 @@ public void CreateGUI()
                 clientConfigSection = new McpClientConfigSection(clientConfigRoot);
             }
 
+            guiCreated = true;
+
             // Initial updates
             RefreshAllData();
         }
@@ -119,6 +159,7 @@ private void OnDisable()
         {
             EditorApplication.update -= OnEditorUpdate;
             OpenWindows.Remove(this);
+            guiCreated = false;
         }
 
         private void OnFocus()
@@ -163,11 +204,11 @@ private void ScheduleHealthCheck()
         {
             EditorApplication.delayCall += async () =>
             {
-                if (this == null)
+                if (this == null || connectionSection == null)
                 {
                     return;
                 }
-                await connectionSection?.VerifyBridgeConnectionAsync();
+                await connectionSection.VerifyBridgeConnectionAsync();
             };
         }
     }