diff --git a/plugins/magpie-setup/hooks/check-upgrade.sh b/plugins/magpie-setup/hooks/check-upgrade.sh
index 22afca3fc..09b281880 100755
--- a/plugins/magpie-setup/hooks/check-upgrade.sh
+++ b/plugins/magpie-setup/hooks/check-upgrade.sh
@@ -72,9 +72,13 @@ fi
 # Once per session, the isolated-setup warning: `setup_preflight` decides
 # whether it applies and prints the notice with it, as hook JSON whose
 # `systemMessage` the user sees. Without python3 the notice goes out alone.
+# `-P` keeps the working directory, which is the project being opened, off
+# `sys.path`: `python3 -m` would otherwise put it ahead of `PYTHONPATH`, and
+# a `setup_preflight/` package committed to that project would run in place
+# of the plugin's own.
 output="$notice"
 if command -v python3 >/dev/null 2>&1; then
-  output="$(PYTHONPATH="$root/skills/setup" python3 -m setup_preflight.isolated session-start \
+  output="$(PYTHONPATH="$root/skills/setup" python3 -P -m setup_preflight.isolated session-start \
     --project-root "${CLAUDE_PROJECT_DIR:-$PWD}" --notice "$notice" 2>/dev/null)" || output="$notice"
 fi
 
diff --git a/plugins/magpie-setup/skills/setup/setup_preflight/isolated_fingerprint.py b/plugins/magpie-setup/skills/setup/setup_preflight/isolated_fingerprint.py
index b37695e8e..09d9a82e6 100644
--- a/plugins/magpie-setup/skills/setup/setup_preflight/isolated_fingerprint.py
+++ b/plugins/magpie-setup/skills/setup/setup_preflight/isolated_fingerprint.py
@@ -21,4 +21,4 @@
 for installs that do not carry the framework source (see `isolated.py`).
 """
 
-FRAMEWORK_FINGERPRINT = "sha256:f11451b59daac4bf"
+FRAMEWORK_FINGERPRINT = "sha256:7e7e47483c71458e"
diff --git a/tools/agent-isolation/container-gateway-hook.sh b/tools/agent-isolation/container-gateway-hook.sh
index 3c2f1b23b..439a68d52 100755
--- a/tools/agent-isolation/container-gateway-hook.sh
+++ b/tools/agent-isolation/container-gateway-hook.sh
@@ -22,8 +22,8 @@
 # socket to talk to. Runs outside the sandbox, like every hook. Never fails
 # the session: every exit is 0, and a missing gateway is silently a no-op.
 #
-#   start   SessionStart — python3 -m container_gateway serve --project=<root> --daemon
-#   stop    SessionEnd   — python3 -m container_gateway stop  --project=<root>
+#   start   SessionStart — python3 -P -m container_gateway serve --project=<root> --daemon
+#   stop    SessionEnd   — python3 -P -m container_gateway stop  --project=<root>
 #
 # Trust model: the hook executes only code from locations the operator installed
 # or pinned, never from the repository being opened. This prevents a malicious repo
@@ -38,6 +38,9 @@
 #   PYTHONPATH is *replaced*, never extended. An inherited entry ahead of (or
 #   behind) the gateway's own source directory can shadow a stdlib module the
 #   package imports, which would run repository code inside the gateway process.
+#   For the same reason the interpreter runs with -P: `python3 -m` puts the
+#   working directory, which is the project being opened, on sys.path ahead of
+#   PYTHONPATH, so a `container_gateway/` package in the project would win.
 #
 #   $MAGPIE_CONTAINER_GATEWAY_ARGS is allow-listed, token by token, against the
 #   flags below (e.g. "--egress require"). Anything else -- notably
@@ -101,9 +104,9 @@ if [[ $action == start ]]; then
             "${0##*/}" "${MAGPIE_CONTAINER_GATEWAY_ARGS}" >&2
         extra=()
     fi
-    cmd=(python3 -m container_gateway serve --project="$root" --daemon "${extra[@]}")
+    cmd=(python3 -P -m container_gateway serve --project="$root" --daemon "${extra[@]}")
 else
-    cmd=(python3 -m container_gateway stop --project="$root")
+    cmd=(python3 -P -m container_gateway stop --project="$root")
 fi
 
 if [[ -n ${MAGPIE_CONTAINER_GATEWAY_DRY_RUN:-} ]]; then
diff --git a/tools/agent-isolation/tests/test_container_gateway_hook.py b/tools/agent-isolation/tests/test_container_gateway_hook.py
index 7ea45ce6c..885a5a1a3 100644
--- a/tools/agent-isolation/tests/test_container_gateway_hook.py
+++ b/tools/agent-isolation/tests/test_container_gateway_hook.py
@@ -47,7 +47,7 @@ def test_start_uses_snapshot_sources(tmp_path: Path) -> None:
     subprocess.run(["git", "init", "-q", str(tmp_path)], check=True)
     done = run("start", tmp_path, home=fake_home)
     assert done.returncode == 0, done.stderr
-    assert done.stdout.strip() == f"PYTHONPATH={src.parent} python3 -m container_gateway serve --project={tmp_path} --daemon"
+    assert done.stdout.strip() == f"PYTHONPATH={src.parent} python3 -P -m container_gateway serve --project={tmp_path} --daemon"
 
 
 def test_start_prefers_env_override_and_appends_args(tmp_path: Path) -> None:
@@ -193,3 +193,12 @@ def test_vetted_extra_args_are_passed_through(tmp_path: Path, args: str) -> None
     assert done.returncode == 0, done.stderr
     assert done.stdout.strip().endswith(f"--daemon {args}")
     assert done.stderr == ""
+
+
+def test_the_project_directory_is_kept_off_sys_path(tmp_path: Path) -> None:
+    """`python3 -m` would put the project, the hook's cwd, ahead of the gateway source."""
+    project, fake_home, _ = _project_with_snapshot(tmp_path)
+    for action in ("start", "stop"):
+        done = run(action, project, home=fake_home)
+        assert done.returncode == 0, done.stderr
+        assert " python3 -P -m container_gateway " in done.stdout
diff --git a/tools/setup-preflight/tests/test_session_hook.py b/tools/setup-preflight/tests/test_session_hook.py
new file mode 100644
index 000000000..edd0e2dee
--- /dev/null
+++ b/tools/setup-preflight/tests/test_session_hook.py
@@ -0,0 +1,56 @@
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements.  See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership.  The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License.  You may obtain a copy of the License at
+#
+#   http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+# KIND, either express or implied.  See the License for the
+# specific language governing permissions and limitations
+# under the License.
+
+"""The plugin's session-start hook runs the plugin's own pre-flight, never the project's."""
+
+from __future__ import annotations
+
+import os
+import subprocess
+from pathlib import Path
+
+PLUGIN_ROOT = Path(__file__).resolve().parents[3] / "plugins" / "magpie-setup"
+HOOK = PLUGIN_ROOT / "hooks" / "check-upgrade.sh"
+
+
+def run_hook(cwd: Path, data: Path) -> subprocess.CompletedProcess[str]:
+    env = {
+        **os.environ,
+        "CLAUDE_PLUGIN_ROOT": str(PLUGIN_ROOT),
+        "CLAUDE_PLUGIN_DATA": str(data),
+        "CLAUDE_PROJECT_DIR": str(cwd),
+    }
+    return subprocess.run(
+        ["bash", str(HOOK)], input="{}", capture_output=True, text=True, env=env, cwd=cwd, check=False
+    )
+
+
+def test_a_package_in_the_project_does_not_shadow_the_plugin(project: Path, tmp_path: Path) -> None:
+    """`python3 -m` would put the opened project, the hook's cwd, ahead of PYTHONPATH."""
+    planted = project / "setup_preflight"
+    planted.mkdir()
+    marker = tmp_path / "planted-ran"
+    code = f"open({str(marker)!r}, 'w').close()\nprint('PLANTED')\n"
+    (planted / "__init__.py").write_text(code, encoding="utf-8")
+    (planted / "isolated.py").write_text(code, encoding="utf-8")
+
+    done = run_hook(project, tmp_path / "data")
+
+    assert done.returncode == 0, done.stderr
+    assert not marker.exists()
+    assert "PLANTED" not in done.stdout
+    assert "Apache Magpie plugin" in done.stdout