diff --git a/packages/cli/src/ui/utils/terminalCapabilityManager.ts b/packages/cli/src/ui/utils/terminalCapabilityManager.ts
index 7867f48e6f..6aeda005dc 100644
--- a/packages/cli/src/ui/utils/terminalCapabilityManager.ts
+++ b/packages/cli/src/ui/utils/terminalCapabilityManager.ts
@@ -13,12 +13,14 @@ import {
   disableModifyOtherKeys,
   enableBracketedPasteMode,
   disableBracketedPasteMode,
+  disableMouseEvents,
 } from '@google/gemini-cli-core';
 import { parseColor } from '../themes/color-utils.js';
 
 export type TerminalBackgroundColor = string | undefined;
 
-const TERMINAL_CLEANUP_SEQUENCE = '\x1b[<u\x1b[>4;0m\x1b[?2004l';
+const TERMINAL_CLEANUP_SEQUENCE =
+  '\x1b[<u\x1b[>4;0m\x1b[?2004l\x1b[?1000l\x1b[?1002l\x1b[?1003l\x1b[?1006l';
 
 export function cleanupTerminalOnExit() {
   try {
@@ -33,6 +35,7 @@ export function cleanupTerminalOnExit() {
   disableKittyKeyboardProtocol();
   disableModifyOtherKeys();
   disableBracketedPasteMode();
+  disableMouseEvents();
 }
 
 export class TerminalCapabilityManager {
diff --git a/packages/cli/src/utils/cleanup.test.ts b/packages/cli/src/utils/cleanup.test.ts
index a722e1a737..0e2454cb82 100644
--- a/packages/cli/src/utils/cleanup.test.ts
+++ b/packages/cli/src/utils/cleanup.test.ts
@@ -72,6 +72,46 @@ describe('cleanup', () => {
     expect(asyncFn).toHaveBeenCalledTimes(1);
   });
 
+  it('should run cleanupFunctions BEFORE draining stdin and BEFORE runSyncCleanup', async () => {
+    const callOrder: string[] = [];
+
+    // Cleanup function
+    registerCleanup(() => {
+      callOrder.push('cleanup');
+    });
+
+    // Sync cleanup function (e.g. setRawMode(false))
+    registerSyncCleanup(() => {
+      callOrder.push('sync');
+    });
+
+    // Mock stdin.resume to track drainStdin
+    const originalResume = process.stdin.resume;
+    process.stdin.resume = vi.fn().mockImplementation(() => {
+      callOrder.push('drain');
+      return process.stdin;
+    });
+
+    // Mock stdin properties for drainStdin
+    const originalIsTTY = process.stdin.isTTY;
+    Object.defineProperty(process.stdin, 'isTTY', {
+      value: true,
+      configurable: true,
+    });
+
+    try {
+      await runExitCleanup();
+    } finally {
+      process.stdin.resume = originalResume;
+      Object.defineProperty(process.stdin, 'isTTY', {
+        value: originalIsTTY,
+        configurable: true,
+      });
+    }
+
+    expect(callOrder).toEqual(['drain', 'drain', 'sync', 'cleanup']);
+  });
+
   it('should continue running cleanup functions even if one throws an error', async () => {
     const errorFn = vi.fn().mockImplementation(() => {
       throw new Error('test error');
diff --git a/packages/cli/src/utils/cleanup.ts b/packages/cli/src/utils/cleanup.ts
index 6185b34fe5..19aa795640 100644
--- a/packages/cli/src/utils/cleanup.ts
+++ b/packages/cli/src/utils/cleanup.ts
@@ -59,7 +59,7 @@ export function registerTelemetryConfig(config: Config) {
 
 export async function runExitCleanup() {
   // drain stdin to prevent printing garbage on exit
-  // https://github.com/google-gemini/gemini-cli/issues/1680
+  // https://github.com/google-gemini/gemini-cli/issues/16801
   await drainStdin();
 
   runSyncCleanup();