diff --git a/code_review_graph/tools/query.py b/code_review_graph/tools/query.py
index d85e1335..9fac54a2 100644
--- a/code_review_graph/tools/query.py
+++ b/code_review_graph/tools/query.py
@@ -373,10 +373,17 @@ def add_result(result: dict[str, Any], edge: Any | None = None) -> None:
                     }
 
         if not node and pattern not in ("consumers_of", "file_summary"):
-            return {
+            # This branch, not the empty-result path below, is where an
+            # unresolved target actually lands for most patterns, so the
+            # not-indexed marker has to be attached here too.
+            unresolved: dict[str, Any] = {
                 "status": "not_found",
                 "summary": f"No node found matching '{target}'.",
             }
+            unresolved_note = empty_query_confidence(store, root, pattern, target, None)
+            if unresolved_note:
+                unresolved["confidence"] = unresolved_note
+            return unresolved
 
         qn = node.qualified_name if node else target
 
diff --git a/code_review_graph/uncertainty.py b/code_review_graph/uncertainty.py
index 91b49e6c..04fbff47 100644
--- a/code_review_graph/uncertainty.py
+++ b/code_review_graph/uncertainty.py
@@ -245,6 +245,19 @@ def not_indexed_note(target: str) -> str:
     )
 
 
+def unresolved_stale_note(target: str) -> str:
+    """Say the target is missing from a graph that predates HEAD.
+
+    A stale graph explains the miss and has a remedy, so it outranks the
+    flat "not indexed" wording, which reads like a permanent limitation.
+    """
+    return _interpolated_target(
+        "graph is stale: no node matching '",
+        target,
+        "'; the graph predates HEAD, so run `code-review-graph update` first",
+    )
+
+
 def _confirmed_note(target: str, current: bool) -> str:
     """Say the zero is a real absence, so the agent can stop searching.
 
@@ -343,6 +356,14 @@ def empty_query_confidence(
     """
     try:
         if node is None:
+            if store.get_stats().total_nodes == 0:
+                return _bounded(
+                    "graph is empty: nothing is indexed, so this 0 says "
+                    "nothing about the code; run `code-review-graph build`"
+                )
+            stale, _unused = _staleness(store, root, None)
+            if stale:
+                return _bounded(unresolved_stale_note(target))
             return _bounded(not_indexed_note(target))
 
         stale, current = _staleness(store, root, getattr(node, "file_path", None))
diff --git a/tests/test_uncertainty.py b/tests/test_uncertainty.py
index 5d75efec..e84066ed 100644
--- a/tests/test_uncertainty.py
+++ b/tests/test_uncertainty.py
@@ -466,3 +466,90 @@ def test_direct_call_returns_none_on_failure(repo, monkeypatch):
         assert empty_query_confidence(
             store, repo, "callers_of", "whatever", None,
         ) is None
+
+
+# ---------------------------------------------------------------------------
+# The not_found branch
+#
+# For every pattern except consumers_of and file_summary, an unresolved target
+# returns early with status "not_found" and never reaches the empty-result
+# path. That branch is where an unindexed target actually lands in production,
+# so the marker has to be attached there too.
+# ---------------------------------------------------------------------------
+
+
+@pytest.mark.parametrize(
+    "pattern",
+    ["callers_of", "callees_of", "imports_of", "tests_for", "inheritors_of"],
+)
+def test_not_found_response_carries_a_marker(repo, pattern):
+    """An unresolved target must never come back as a bare not_found."""
+    result = query_graph(
+        pattern=pattern, target="NoSuchSymbol", repo_root=str(repo),
+    )
+
+    assert result["status"] == "not_found"
+    assert result["confidence"]
+    assert "NoSuchSymbol" in result["confidence"]
+
+
+def test_unresolved_target_on_a_stale_graph_says_stale_not_unindexed(repo, monkeypatch):
+    """A stale graph explains the miss and has a remedy, so it must win.
+
+    Calling it "not indexed" reads like a permanent limitation and sends the
+    agent looking for a parser gap that is not there.
+    """
+    with _store(repo) as store:
+        store.set_metadata("git_head_sha", "0" * 40)
+        store.commit()
+
+    monkeypatch.setattr(uncertainty, "_live_git_head", lambda root: "f" * 40)
+    result = query_graph(
+        pattern="callers_of", target="NoSuchSymbol", repo_root=str(repo),
+    )
+
+    assert "stale" in result["confidence"]
+    assert "update" in result["confidence"]
+    assert "not indexed" not in result["confidence"]
+
+
+def test_unresolved_target_on_a_current_graph_says_not_indexed(repo, monkeypatch):
+    """With currency established, not-indexed is the honest answer."""
+    with _store(repo) as store:
+        store.set_metadata("git_head_sha", "a" * 40)
+        store.commit()
+
+    monkeypatch.setattr(uncertainty, "_live_git_head", lambda root: "a" * 40)
+    result = query_graph(
+        pattern="callers_of", target="NoSuchSymbol", repo_root=str(repo),
+    )
+
+    assert "not indexed" in result["confidence"]
+    assert "stale" not in result["confidence"]
+
+
+def test_unresolved_target_on_an_empty_graph_says_build(tmp_path):
+    """Nothing indexed at all is a build problem, not a missing symbol."""
+    root = (tmp_path / "empty").resolve()
+    (root / ".code-review-graph").mkdir(parents=True)
+    (root / ".git").mkdir()
+    GraphStore(root / ".code-review-graph" / "graph.db").close()
+
+    result = query_graph(
+        pattern="callers_of", target="Anything", repo_root=str(root),
+    )
+
+    assert "graph is empty" in result["confidence"]
+    assert "build" in result["confidence"]
+
+
+def test_resolved_target_with_results_still_has_no_marker(repo):
+    """The token-budget guarantee holds on the not_found-adjacent path too."""
+    result = query_graph(
+        pattern="callers_of",
+        target=f"{(repo / 'auth.py').as_posix()}::login",
+        repo_root=str(repo),
+    )
+
+    assert result["result_count"] >= 1
+    assert "confidence" not in result