diff --git a/extensions/agent-context/scripts/bash/update-agent-context.sh b/extensions/agent-context/scripts/bash/update-agent-context.sh
index b7121a2f64..b66eafc09f 100755
--- a/extensions/agent-context/scripts/bash/update-agent-context.sh
+++ b/extensions/agent-context/scripts/bash/update-agent-context.sh
@@ -307,16 +307,24 @@ import sys
 from pathlib import Path
 root = Path(sys.argv[1]).resolve()
 specs = root / "specs"
-plans = sorted(
-    specs.glob("*/plan.md"),
-    key=lambda p: p.stat().st_mtime,
-    reverse=True,
-)
-if plans:
+
+def _resolved_rel(p):
+    # Resolve symlinks before checking containment: relative_to() is lexical
+    # and would otherwise accept a plan reached through a specs/ symlink that
+    # points outside the project, emitting an in-project-looking path for an
+    # out-of-project file (or picking it as "most recent").
     try:
-        print(plans[0].relative_to(root).as_posix())
-    except ValueError:
-        print("")
+        return p.resolve().relative_to(root)
+    except (OSError, ValueError):
+        return None
+
+# Recurse (rather than the old one-level specs/*/plan.md glob) so scoped layouts
+# created via SPECIFY_FEATURE_DIRECTORY, e.g. specs/<scope>/<feature>/plan.md,
+# are still discovered when feature.json is absent (#3024).
+candidates = [(p, rel) for p in specs.rglob("plan.md") if (rel := _resolved_rel(p))]
+candidates.sort(key=lambda pr: pr[0].stat().st_mtime, reverse=True)
+if candidates:
+    print(candidates[0][1].as_posix())
 else:
     print("")
 PY
diff --git a/extensions/agent-context/scripts/powershell/update-agent-context.ps1 b/extensions/agent-context/scripts/powershell/update-agent-context.ps1
index 98a55c55fd..29f8e68097 100644
--- a/extensions/agent-context/scripts/powershell/update-agent-context.ps1
+++ b/extensions/agent-context/scripts/powershell/update-agent-context.ps1
@@ -426,9 +426,11 @@ if (-not $PlanPath) {
     if (-not $PlanPath) {
         try {
             $specsDir = Join-Path $ProjectRoot 'specs'
-            $candidate = Get-ChildItem -Path $specsDir -Directory -ErrorAction SilentlyContinue |
-                ForEach-Object { Get-Item -LiteralPath (Join-Path $_.FullName 'plan.md') -ErrorAction SilentlyContinue } |
-                Where-Object { $_ } |
+            # Recurse (rather than the old one-level specs/*/plan.md scan) so scoped
+            # layouts created via SPECIFY_FEATURE_DIRECTORY, e.g.
+            # specs/<scope>/<feature>/plan.md, are still discovered when
+            # feature.json is absent (#3024).
+            $candidate = Get-ChildItem -Path $specsDir -Filter 'plan.md' -File -Recurse -ErrorAction SilentlyContinue |
                 Sort-Object LastWriteTime -Descending |
                 Select-Object -First 1
             if ($candidate) {
diff --git a/tests/extensions/test_extension_agent_context.py b/tests/extensions/test_extension_agent_context.py
index f99d449401..bcfb208685 100644
--- a/tests/extensions/test_extension_agent_context.py
+++ b/tests/extensions/test_extension_agent_context.py
@@ -25,6 +25,14 @@
 POWERSHELL = (
     shutil.which("pwsh") or shutil.which("powershell.exe") or shutil.which("powershell")
 )
+# On Windows, prefer the built-in Windows PowerShell 5.1 (.NET Framework) when a
+# test needs to exercise a 5.1-specific code path; fall back to whatever
+# POWERSHELL resolves to elsewhere.
+WINDOWS_POWERSHELL = (
+    (shutil.which("powershell.exe") or shutil.which("powershell") or POWERSHELL)
+    if os.name == "nt"
+    else POWERSHELL
+)
 
 
 def _write_ext_config(project_root: Path, **overrides: object) -> None:
@@ -279,12 +287,14 @@ def shlex_quote(value: str) -> str:
     return "'" + value.replace("'", "'\"'\"'") + "'"
 
 
-def _run_powershell_agent_context_script(project_root: Path) -> subprocess.CompletedProcess:
+def _run_powershell_agent_context_script(
+    project_root: Path, powershell: str | None = None
+) -> subprocess.CompletedProcess:
     script = EXT_DIR / "scripts" / "powershell" / "update-agent-context.ps1"
     env = _bundled_script_env(project_root)
     return subprocess.run(
         [
-            POWERSHELL,
+            powershell or POWERSHELL,
             "-NoProfile",
             "-ExecutionPolicy",
             "Bypass",
@@ -412,6 +422,29 @@ def test_bash_script_deduplicates_context_files_in_order(self, tmp_path):
         assert output.count("agent-context: updated CLAUDE.md") == 1
         assert "agent-context: updated agents.md" not in output
 
+    @requires_bash
+    def test_bash_script_discovers_nested_plan(self, tmp_path):
+        """Plan discovery recurses into scoped layouts (#3024)."""
+        project = tmp_path / "project"
+        project.mkdir()
+        _install_agent_context_config(
+            project,
+            context_file="AGENTS.md",
+            context_files=[],
+        )
+        plan = project / "specs" / "scope" / "001-feature" / "plan.md"
+        plan.parent.mkdir(parents=True)
+        plan.write_text("# Plan\n", encoding="utf-8")
+
+        result = _run_bash_agent_context_script(project)
+
+        assert result.returncode == 0, result.stderr + result.stdout
+        text = (project / "AGENTS.md").read_text(encoding="utf-8")
+        # The old one-level glob (specs/*/plan.md) would find nothing here, so no
+        # "at" line would be emitted. Normalize separators before matching: on
+        # MSYS bash the emitted path may be absolute with backslashes.
+        assert "specs/scope/001-feature/plan.md" in text.replace("\\", "/")
+
     @requires_bash
     def test_bash_script_falls_back_from_invalid_speckit_python(self, tmp_path):
         project = tmp_path / "project"
@@ -484,6 +517,33 @@ def test_powershell_script_deduplicates_context_files_in_order(self, tmp_path):
         assert output.count("agent-context: updated CLAUDE.md") == 1
         assert "agent-context: updated agents.md" not in output
 
+    @pytest.mark.skipif(WINDOWS_POWERSHELL is None, reason="PowerShell not available")
+    def test_powershell_script_discovers_nested_plan(self, tmp_path):
+        """Plan discovery recurses into scoped layouts (#3024).
+
+        The relative-path fix this covers is specific to Windows PowerShell 5.1
+        (.NET Framework), so prefer ``powershell.exe`` over ``pwsh`` here to
+        actually exercise that failure mode on Windows.
+        """
+        project = tmp_path / "project"
+        project.mkdir()
+        _install_agent_context_config(
+            project,
+            context_file="AGENTS.md",
+            context_files=[],
+        )
+        plan = project / "specs" / "scope" / "001-feature" / "plan.md"
+        plan.parent.mkdir(parents=True)
+        plan.write_text("# Plan\n", encoding="utf-8")
+
+        result = _run_powershell_agent_context_script(
+            project, powershell=WINDOWS_POWERSHELL
+        )
+
+        assert result.returncode == 0, result.stderr + result.stdout
+        text = (project / "AGENTS.md").read_text(encoding="utf-8")
+        assert "at specs/scope/001-feature/plan.md" in text
+
     @pytest.mark.skipif(POWERSHELL is None, reason="PowerShell not available")
     def test_powershell_script_falls_back_from_invalid_speckit_python(self, tmp_path):
         project = tmp_path / "project"