diff --git a/desktop/src/stores/chatStore.test.ts b/desktop/src/stores/chatStore.test.ts
index 0692edec..b903a265 100644
--- a/desktop/src/stores/chatStore.test.ts
+++ b/desktop/src/stores/chatStore.test.ts
@@ -3982,6 +3982,67 @@ describe('chatStore history mapping', () => {
     })
   })
 
+  it('replaces orphan thinking with authoritative history when a reconnected turn completes', async () => {
+    vi.mocked(sessionsApi.getMessages).mockClear()
+    vi.mocked(sessionsApi.getMessages).mockResolvedValue({
+      messages: [
+        {
+          id: 'persisted-user',
+          type: 'user',
+          timestamp: '2026-07-11T00:00:00.000Z',
+          content: 'Finish the foreground task',
+        },
+        {
+          id: 'persisted-assistant',
+          type: 'assistant',
+          timestamp: '2026-07-11T00:00:01.000Z',
+          content: [{ type: 'text', text: 'Foreground task finished.' }],
+        },
+      ],
+    })
+    useChatStore.setState({
+      sessions: {
+        [TEST_SESSION_ID]: makeSession({
+          chatState: 'idle',
+          messages: [],
+        }),
+      },
+    })
+
+    useChatStore.getState().handleServerMessage(TEST_SESSION_ID, {
+      type: 'session_state',
+      turnState: 'running',
+    })
+    await vi.waitFor(() => {
+      expect(useChatStore.getState().sessions[TEST_SESSION_ID]?.messages).toHaveLength(2)
+    })
+
+    // The task_notification that should suppress this output arrived while
+    // the renderer was disconnected, so only the late follow-up is observed.
+    useChatStore.getState().handleServerMessage(TEST_SESSION_ID, {
+      type: 'thinking',
+      text: 'orphan background follow-up thinking',
+    })
+    expect(useChatStore.getState().sessions[TEST_SESSION_ID]?.messages).toContainEqual(
+      expect.objectContaining({
+        type: 'thinking',
+        content: 'orphan background follow-up thinking',
+      }),
+    )
+
+    useChatStore.getState().handleServerMessage(TEST_SESSION_ID, {
+      type: 'message_complete',
+      usage: { input_tokens: 5, output_tokens: 8 },
+    })
+
+    await vi.waitFor(() => {
+      expect(useChatStore.getState().sessions[TEST_SESSION_ID]?.messages).not.toContainEqual(
+        expect.objectContaining({ type: 'thinking' }),
+      )
+    })
+    expect(sessionsApi.getMessages).toHaveBeenCalledTimes(2)
+  })
+
   it('keeps the tab running for background agents when reconnect reconciliation finds the foreground idle', () => {
     useChatStore.setState({
       sessions: {
diff --git a/desktop/src/stores/chatStore.ts b/desktop/src/stores/chatStore.ts
index 1a3e54ec..bfabed47 100644
--- a/desktop/src/stores/chatStore.ts
+++ b/desktop/src/stores/chatStore.ts
@@ -129,6 +129,7 @@ export type PerSessionState = {
   backgroundAgentTasks?: Record<string, BackgroundAgentTask>
   stoppingBackgroundTaskIds?: Record<string, boolean>
   suppressNextTaskNotificationResponse?: boolean
+  replaceHistoryOnCompletion?: boolean
   activeGoal?: ActiveGoalState | null
   elapsedTimer: ReturnType<typeof setInterval> | null
   composerPrefill?: {
@@ -169,6 +170,7 @@ const DEFAULT_SESSION_STATE: PerSessionState = {
   backgroundAgentTasks: {},
   stoppingBackgroundTaskIds: {},
   suppressNextTaskNotificationResponse: false,
+  replaceHistoryOnCompletion: false,
   activeGoal: null,
   elapsedTimer: null,
   composerPrefill: null,
@@ -883,6 +885,24 @@ function refreshCompletedTranscriptHistory(
   })
 }
 
+function reconcileCompletedTranscriptHistory(
+  get: () => ChatStore,
+  sessionId: string,
+  replaceHistory: boolean,
+): void {
+  if (!replaceHistory) {
+    refreshCompletedTranscriptHistory(get, sessionId)
+    return
+  }
+
+  const session = get().sessions[sessionId]
+  if (!session) return
+  void get().reloadHistory(sessionId, {
+    messages: session.messages,
+    backgroundAgentTasks: session.backgroundAgentTasks,
+  })
+}
+
 function normalizeMemoryEventFiles(data: unknown): MemoryEventFile[] {
   if (!data || typeof data !== 'object') return []
   const writtenPaths = (data as { writtenPaths?: unknown }).writtenPaths
@@ -1199,6 +1219,7 @@ export const useChatStore = create<ChatStore>((set, get) => ({
             chatState: 'thinking',
             elapsedSeconds: 0,
             suppressNextTaskNotificationResponse: false,
+            replaceHistoryOnCompletion: false,
             streamingText: '',
             streamingResponseChars: 0,
             statusVerb: isMemberSession ? '' : randomSpinnerVerb(),
@@ -1669,6 +1690,7 @@ export const useChatStore = create<ChatStore>((set, get) => ({
             .filter((message) => message.id !== messageId),
           ...(pendingText.trim() ? { streamingText: '' } : {}),
           suppressNextTaskNotificationResponse: false,
+          replaceHistoryOnCompletion: false,
         }
       }),
     }))
@@ -1692,6 +1714,7 @@ export const useChatStore = create<ChatStore>((set, get) => ({
       apiRetry: null,
       streamingFallback: null,
       suppressNextTaskNotificationResponse: false,
+      replaceHistoryOnCompletion: false,
       queuedUserMessages: [],
     })) }))
   },
@@ -1765,6 +1788,7 @@ export const useChatStore = create<ChatStore>((set, get) => ({
               apiRetry: null,
               streamingFallback: null,
               statusVerb: '',
+              replaceHistoryOnCompletion: true,
             }
           })
           useTabStore.getState().updateTabStatus(sessionId, 'running')
@@ -2388,9 +2412,14 @@ export const useChatStore = create<ChatStore>((set, get) => ({
             streamingText: '',
             streamingToolInput: '',
             suppressNextTaskNotificationResponse: false,
+            replaceHistoryOnCompletion: false,
           }))
           useTabStore.getState().updateTabStatus(sessionId, hasRunningBackgroundAgents ? 'running' : 'idle')
-          refreshCompletedTranscriptHistory(get, sessionId)
+          reconcileCompletedTranscriptHistory(
+            get,
+            sessionId,
+            session.replaceHistoryOnCompletion === true,
+          )
           for (const queuedMessage of get().sessions[sessionId]?.queuedUserMessages ?? []) {
             get().sendQueuedUserMessage(sessionId, queuedMessage.id)
           }
@@ -2425,6 +2454,7 @@ export const useChatStore = create<ChatStore>((set, get) => ({
           elapsedTimer: null,
           apiRetry: null,
           streamingFallback: null,
+          replaceHistoryOnCompletion: false,
         }))
         useTabStore.getState().updateTabStatus(sessionId, hasRunningBackgroundAgents ? 'running' : 'idle')
         const notification = wasAgentRunning && appendedCompletionMessage
@@ -2439,7 +2469,11 @@ export const useChatStore = create<ChatStore>((set, get) => ({
             target: { type: 'session', sessionId },
           })
         }
-        refreshCompletedTranscriptHistory(get, sessionId)
+        reconcileCompletedTranscriptHistory(
+          get,
+          sessionId,
+          session.replaceHistoryOnCompletion === true,
+        )
         for (const queuedMessage of get().sessions[sessionId]?.queuedUserMessages ?? []) {
           get().sendQueuedUserMessage(sessionId, queuedMessage.id)
         }
@@ -2457,6 +2491,7 @@ export const useChatStore = create<ChatStore>((set, get) => ({
             ...(pendingText.trim() ? { streamingText: '' } : {}),
             activeThinkingId: null,
             suppressNextTaskNotificationResponse: false,
+            replaceHistoryOnCompletion: false,
           }
         })
         break