diff --git a/packages/cli/src/ui/AppContainer.test.tsx b/packages/cli/src/ui/AppContainer.test.tsx
index 6c69aa332f..1e0911bb2e 100644
--- a/packages/cli/src/ui/AppContainer.test.tsx
+++ b/packages/cli/src/ui/AppContainer.test.tsx
@@ -3196,6 +3196,92 @@ describe('AppContainer State Management', () => {
       unmount();
     });
 
+    it('sets activeExtensionContext when an extension command WITH a plan dir is executed', async () => {
+      const { checkPermissions } = await import(
+        './hooks/atCommandProcessor.js'
+      );
+      vi.mocked(checkPermissions).mockResolvedValue([]);
+
+      mockedUseSlashCommandProcessor.mockReturnValue({
+        handleSlashCommand: vi.fn(),
+        slashCommands: [
+          {
+            name: 'conductor:setup',
+            extensionName: 'conductor',
+            description: 'test',
+            action: vi.fn(),
+          },
+        ],
+        pendingHistoryItems: [],
+        commandContext: {},
+        shellConfirmationRequest: null,
+        confirmationRequest: null,
+      });
+
+      const spyHasExtensionPlanDir = vi
+        .spyOn(mockConfig, 'hasExtensionPlanDir')
+        .mockReturnValue(true);
+      const spySetActiveExtensionContext = vi.spyOn(
+        mockConfig,
+        'setActiveExtensionContext',
+      );
+
+      const { unmount } = await act(async () => renderAppContainer());
+
+      expect(capturedUIActions).toBeTruthy();
+
+      await act(async () =>
+        capturedUIActions.handleFinalSubmit('/conductor:setup'),
+      );
+
+      expect(spyHasExtensionPlanDir).toHaveBeenCalledWith('conductor');
+      expect(spySetActiveExtensionContext).toHaveBeenCalledWith('conductor');
+
+      unmount();
+    });
+
+    it('clears activeExtensionContext when an extension command WITHOUT a plan dir is executed', async () => {
+      const { checkPermissions } = await import(
+        './hooks/atCommandProcessor.js'
+      );
+      vi.mocked(checkPermissions).mockResolvedValue([]);
+
+      mockedUseSlashCommandProcessor.mockReturnValue({
+        handleSlashCommand: vi.fn(),
+        slashCommands: [
+          {
+            name: 'other:cmd',
+            extensionName: 'other',
+            description: 'test',
+            action: vi.fn(),
+          },
+        ],
+        pendingHistoryItems: [],
+        commandContext: {},
+        shellConfirmationRequest: null,
+        confirmationRequest: null,
+      });
+
+      const spyHasExtensionPlanDir = vi
+        .spyOn(mockConfig, 'hasExtensionPlanDir')
+        .mockReturnValue(false);
+      const spySetActiveExtensionContext = vi.spyOn(
+        mockConfig,
+        'setActiveExtensionContext',
+      );
+
+      const { unmount } = await act(async () => renderAppContainer());
+
+      expect(capturedUIActions).toBeTruthy();
+
+      await act(async () => capturedUIActions.handleFinalSubmit('/other:cmd'));
+
+      expect(spyHasExtensionPlanDir).toHaveBeenCalledWith('other');
+      expect(spySetActiveExtensionContext).toHaveBeenCalledWith(undefined);
+
+      unmount();
+    });
+
     it('clears activeExtensionContext when /plan is explicitly executed', async () => {
       const { checkPermissions } = await import(
         './hooks/atCommandProcessor.js'
@@ -3228,6 +3314,38 @@ describe('AppContainer State Management', () => {
 
       unmount();
     });
+
+    it('does NOT clear activeExtensionContext when a standard non-plan command is executed', async () => {
+      const { checkPermissions } = await import(
+        './hooks/atCommandProcessor.js'
+      );
+      vi.mocked(checkPermissions).mockResolvedValue([]);
+
+      mockedUseSlashCommandProcessor.mockReturnValue({
+        handleSlashCommand: vi.fn(),
+        slashCommands: [{ name: 'help', description: 'test', action: vi.fn() }],
+        pendingHistoryItems: [],
+        commandContext: {},
+        shellConfirmationRequest: null,
+        confirmationRequest: null,
+      });
+
+      const spySetActiveExtensionContext = vi.spyOn(
+        mockConfig,
+        'setActiveExtensionContext',
+      );
+
+      const { unmount } = await act(async () => renderAppContainer());
+
+      expect(capturedUIActions).toBeTruthy();
+
+      await act(async () => capturedUIActions.handleFinalSubmit('/help'));
+
+      // It should not touch the context at all
+      expect(spySetActiveExtensionContext).not.toHaveBeenCalled();
+
+      unmount();
+    });
   });
 
   describe('Overflow Hint Handling', () => {
diff --git a/packages/cli/src/ui/AppContainer.tsx b/packages/cli/src/ui/AppContainer.tsx
index d7c5c2cc5d..73da24cdef 100644
--- a/packages/cli/src/ui/AppContainer.tsx
+++ b/packages/cli/src/ui/AppContainer.tsx
@@ -1349,6 +1349,8 @@ Logging in with Google... Restarting Gemini CLI to continue.
         if (parsedCommand.extensionContext) {
           if (config.hasExtensionPlanDir(parsedCommand.extensionContext)) {
             config.setActiveExtensionContext(parsedCommand.extensionContext);
+          } else {
+            config.setActiveExtensionContext(undefined);
           }
         } else if (parsedCommand.commandToExecute?.name === 'plan') {
           config.setActiveExtensionContext(undefined);