diff --git a/bootstrap/bootstrap.py b/bootstrap/bootstrap.py
index 6f60205..3966588 100644
--- a/bootstrap/bootstrap.py
+++ b/bootstrap/bootstrap.py
@@ -228,20 +228,15 @@
   that is using the bootstrapped Python!
   """
   root_contents = os.listdir(ROOT_DIR)
-  cleanup_paths = ('win_tools-*_bin', 'python27*_bin', 'git-*_bin',
-                   'bootstrap-*_bin', 'python.bat', 'python3.bat')
-  for f in cleanup_paths:
+  for f in ('win_tools-*_bin', 'python27*_bin', 'git-*_bin', 'bootstrap-*_bin'):
     for entry in fnmatch.filter(root_contents, f):
       full_entry = os.path.join(ROOT_DIR, entry)
-      if full_entry == skip_dir:
+      if full_entry == skip_dir or not os.path.isdir(full_entry):
         continue
 
       logging.info('Cleaning up old installation %r', entry)
       if not _toolchain_in_use(full_entry):
-        if os.path.isdir(full_entry):
-          _safe_rmtree(full_entry)
-        else:
-          os.remove(full_entry)
+        _safe_rmtree(full_entry)
       else:
         logging.info('Toolchain at %r is in-use; skipping', full_entry)
 
@@ -326,6 +321,8 @@
     git_postprocess(template, os.path.join(bootstrap_dir, 'git'))
     templates = [
         ('git-bash.template.sh', 'git-bash', ROOT_DIR),
+        ('python27.bat', 'python.bat', ROOT_DIR),
+        ('python3.bat', 'python3.bat', ROOT_DIR),
     ]
     for src_name, dst_name, dst_dir in templates:
       # Re-evaluate and regenerate our root templated files.
diff --git a/git-runhooks b/git-runhooks
index e487447..5bb503e 100755
--- a/git-runhooks
+++ b/git-runhooks
@@ -15,7 +15,7 @@
 kernel_name=$(uname -s)
 if [ "${kernel_name:0:5}" = "MINGW" ]; then
   dir="${0%\\*}"
-  cmd "/C ${dir}\\python2-bin\\python.bat ${dir}\\gclient.py runhooks --spec=$gclient_spec"
+  cmd "/C ${dir}\\python.bat ${dir}\\gclient.py runhooks --spec=$gclient_spec"
 else
   dir="$(dirname $0)"
   PYTHONDONTWRITEBYTECODE=1 exec python "$dir/gclient.py" runhooks --spec="$gclient_spec"
diff --git a/vpython.bat b/vpython.bat
index a5c7d63..ca5fe39 100644
--- a/vpython.bat
+++ b/vpython.bat
@@ -3,10 +3,5 @@
 :: Use of this source code is governed by a BSD-style license that can be
 :: found in the LICENSE file.
 
-:: TODO(crbug.com/1003139): Remove.
-:: Add Python 3 to PATH to work around crbug.com/1003139.
-for /f %%i in (%~dp0python_bin_reldir.txt) do set PYTHON2_BIN_RELDIR=%%i
-set PATH=%~dp0%PYTHON2_BIN_RELDIR%;%~dp0%PYTHON2_BIN_RELDIR%\Scripts;%~dp0%PYTHON2_BIN_RELDIR%\DLLs;%PATH%
-
 call "%~dp0\cipd_bin_setup.bat" > nul 2>&1
-"%~dp0\.cipd_bin\vpython.exe" -vpython-interpreter "%~dp0\%PYTHON2_BIN_RELDIR%\python.exe" %*
+"%~dp0\.cipd_bin\vpython.exe" -vpython-interpreter "%~dp0\python.bat" %*