diff --git a/packages/cli/src/test-utils/mockConfig.ts b/packages/cli/src/test-utils/mockConfig.ts
index daf109d928..3f85690d45 100644
--- a/packages/cli/src/test-utils/mockConfig.ts
+++ b/packages/cli/src/test-utils/mockConfig.ts
@@ -23,6 +23,8 @@ export const createMockConfig = (overrides: Partial<Config> = {}): Config =>
     isInteractive: vi.fn(() => false),
     isInitialized: vi.fn(() => true),
     setTerminalBackground: vi.fn(),
+    setActiveExtensionContext: vi.fn(),
+    hasExtensionPlanDir: vi.fn(() => true),
     storage: {
       getProjectTempDir: vi.fn().mockReturnValue('/tmp/gemini-test'),
       initialize: vi.fn().mockResolvedValue(undefined),
diff --git a/packages/cli/src/ui/AppContainer.test.tsx b/packages/cli/src/ui/AppContainer.test.tsx
index 0e436cc645..051e8834f1 100644
--- a/packages/cli/src/ui/AppContainer.test.tsx
+++ b/packages/cli/src/ui/AppContainer.test.tsx
@@ -3182,6 +3182,39 @@ describe('AppContainer State Management', () => {
       );
       unmount();
     });
+
+    it('clears activeExtensionContext when /plan is explicitly executed', async () => {
+      const { checkPermissions } = await import(
+        './hooks/atCommandProcessor.js'
+      );
+      vi.mocked(checkPermissions).mockResolvedValue([]);
+
+      mockedUseSlashCommandProcessor.mockReturnValue({
+        handleSlashCommand: vi.fn(),
+        slashCommands: [{ name: 'plan', 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('/plan my task'),
+      );
+
+      expect(spySetActiveExtensionContext).toHaveBeenCalledWith(undefined);
+
+      unmount();
+    });
   });
 
   describe('Overflow Hint Handling', () => {
diff --git a/packages/cli/src/ui/AppContainer.tsx b/packages/cli/src/ui/AppContainer.tsx
index ee0d49f2be..2a34029e4d 100644
--- a/packages/cli/src/ui/AppContainer.tsx
+++ b/packages/cli/src/ui/AppContainer.tsx
@@ -1313,9 +1313,13 @@ Logging in with Google... Restarting Gemini CLI to continue.
         slashCommands ?? [],
       );
 
-      if (parsedCommand.extensionContext && config) {
-        if (config.hasExtensionPlanDir(parsedCommand.extensionContext)) {
-          config.setActiveExtensionContext(parsedCommand.extensionContext);
+      if (config) {
+        if (parsedCommand.extensionContext) {
+          if (config.hasExtensionPlanDir(parsedCommand.extensionContext)) {
+            config.setActiveExtensionContext(parsedCommand.extensionContext);
+          }
+        } else if (parsedCommand.commandToExecute?.name === 'plan') {
+          config.setActiveExtensionContext(undefined);
         }
       }
 
diff --git a/packages/core/src/config/storage.test.ts b/packages/core/src/config/storage.test.ts
index b5b8c26841..e695ae5d9b 100644
--- a/packages/core/src/config/storage.test.ts
+++ b/packages/core/src/config/storage.test.ts
@@ -358,6 +358,26 @@ describe('Storage – additional helpers', () => {
         expectedError:
           "Custom plans directory 'symlink-to-outside' resolves to '/outside/project/root', which is outside the project root '/tmp/project'.",
       },
+      {
+        name: 'non-existent plan dir in a symlinked project root',
+        customDir: 'new-plans',
+        setup: () => {
+          vi.mocked(fs.realpathSync).mockImplementation((p: fs.PathLike) => {
+            const pStr = p.toString();
+            if (pStr === projectRoot) {
+              return '/private/tmp/project';
+            }
+            if (pStr.includes('new-plans')) {
+              const err = new Error('ENOENT') as NodeJS.ErrnoException;
+              err.code = 'ENOENT';
+              throw err;
+            }
+            return pStr;
+          });
+          return () => vi.mocked(fs.realpathSync).mockRestore();
+        },
+        expected: path.resolve(projectRoot, 'new-plans'),
+      },
     ];
 
     testCases.forEach(({ name, customDir, expected, expectedError, setup }) => {
diff --git a/packages/core/src/config/storage.ts b/packages/core/src/config/storage.ts
index bd7ce303e2..63d3921c58 100644
--- a/packages/core/src/config/storage.ts
+++ b/packages/core/src/config/storage.ts
@@ -333,6 +333,8 @@ export class Storage {
         ) {
           throw e;
         }
+        // Construct the fallback path safely against the real project root
+        realResolvedPath = path.resolve(realProjectRoot, customDir);
       }
 
       if (!isSubpath(realProjectRoot, realResolvedPath)) {