diff --git a/cli.py b/cli.py
index 489068c783107..6a81546911a4c 100644
--- a/cli.py
+++ b/cli.py
@@ -18126,6 +18126,10 @@ def main(
     
     # Handle single query mode
     if query or image:
+        # One-shot mode: no between-turns MCP late-binding refresh, so the
+        # agent must wait the full MCP cold-start bound before its first
+        # (and only) tool snapshot. See #51316.
+        cli._single_query_mode = True
         if not cli._claim_active_session("cli", stderr=bool(quiet)):
             sys.exit(1)
         try:
diff --git a/hermes_cli/cli_agent_setup_mixin.py b/hermes_cli/cli_agent_setup_mixin.py
index 0cd437645e8ea..29173eda409ae 100644
--- a/hermes_cli/cli_agent_setup_mixin.py
+++ b/hermes_cli/cli_agent_setup_mixin.py
@@ -246,9 +246,12 @@ class CLIAgentSetupMixin:
         if not self._ensure_runtime_credentials():
             return False
 
-        from hermes_cli.mcp_startup import wait_for_mcp_discovery
+        from hermes_cli.mcp_startup import ensure_mcp_discovery_before_agent_build
 
-        wait_for_mcp_discovery()
+        ensure_mcp_discovery_before_agent_build(
+            logger=logger,
+            single_query=getattr(self, "_single_query_mode", False),
+        )
 
         # Initialize SQLite session store for CLI sessions (if not already done in __init__)
         if self._session_db is None:
diff --git a/hermes_cli/config_defaults.py b/hermes_cli/config_defaults.py
index 872038e4dc283..3ecf0b85d1e80 100644
--- a/hermes_cli/config_defaults.py
+++ b/hermes_cli/config_defaults.py
@@ -463,6 +463,16 @@ DEFAULT_CONFIG = {
     # small so a slow/dead server adds little to first-response latency.
     "mcp_discovery_timeout": 1.5,
 
+    # Single-query (``hermes -q/-z "..."``) variant of mcp_discovery_timeout.
+    # In one-shot mode there is only ONE turn, so the between-turns late-binding
+    # refresh never runs: a server that misses the small interactive bound is
+    # invisible to the LLM for the whole session.  This larger bound gives slow
+    # cold-start servers (npx, uvx, remote HTTP) a chance to land in the one
+    # tool snapshot.  ``thread.join(timeout)`` returns the instant discovery
+    # completes, so reachable servers only wait for their real handshake time
+    # while unavailable servers remain bounded.
+    "mcp_single_query_discovery_timeout": 15.0,
+
     # MCP runtime behavior (distinct from the per-server definitions in
     # mcp_servers: and from the auxiliary.mcp side-LLM task settings).
     "mcp": {
diff --git a/hermes_cli/mcp_startup.py b/hermes_cli/mcp_startup.py
index 82839d933b67c..a350f648d6ccc 100644
--- a/hermes_cli/mcp_startup.py
+++ b/hermes_cli/mcp_startup.py
@@ -114,25 +114,44 @@ def start_background_mcp_discovery(*, logger, thread_name: str) -> None:
         thread.start()
 
 
-def _resolve_discovery_timeout(explicit: "float | None") -> float:
+def _resolve_discovery_timeout(
+    explicit: "float | None", *, single_query: bool = False
+) -> float:
     """Resolve the MCP discovery wait bound: explicit arg > config > default.
 
     Reads ``mcp_discovery_timeout`` from config.yaml, defaulting to the value in
     ``DEFAULT_CONFIG`` (single source of truth) when the key is absent. Kept lazy
     and fail-safe — a missing/invalid value or a broken config falls back to a
     short safe bound so startup can never hang or crash.
+
+    When ``single_query`` is True (``hermes -z "..."`` / ``-q``), the larger
+    ``mcp_single_query_discovery_timeout`` bound is used instead. In single-query
+    mode there is only ONE turn, so the between-turns late-binding refresh never
+    runs — a server that misses the small interactive bound would be invisible to
+    the LLM for the whole session. The wait still returns the instant discovery
+    completes (see ``wait_for_mcp_discovery``), so fast servers pay ~0s; the
+    larger bound only caps how long a genuinely slow cold-start may block.
     """
     if explicit is not None:
         return explicit
+    key = (
+        "mcp_single_query_discovery_timeout"
+        if single_query
+        else "mcp_discovery_timeout"
+    )
+    fallback = 15.0 if single_query else 1.5
     try:
         from hermes_cli.config import load_config, DEFAULT_CONFIG
 
-        default = float(DEFAULT_CONFIG.get("mcp_discovery_timeout", 1.5))
-        raw = (load_config() or {}).get("mcp_discovery_timeout", default)
-        val = float(raw)
-        return val if val > 0 else default
+        default = float(DEFAULT_CONFIG.get(key, fallback))
+        try:
+            raw = (load_config() or {}).get(key, default)
+            val = float(raw)
+            return val if val > 0 else default
+        except Exception:
+            return default
     except Exception:
-        return 1.5
+        return fallback
 
 
 def _discover_mcp_tools_without_interactive_oauth() -> None:
@@ -148,7 +167,9 @@ def _discover_mcp_tools_without_interactive_oauth() -> None:
         discover_mcp_tools()
 
 
-def wait_for_mcp_discovery(timeout: "float | None" = None) -> None:
+def wait_for_mcp_discovery(
+    timeout: "float | None" = None, *, single_query: bool = False
+) -> None:
     """Wait for background MCP discovery before the first tool snapshot.
 
     ``thread.join(timeout)`` returns the INSTANT discovery completes, so this
@@ -157,11 +178,15 @@ def wait_for_mcp_discovery(timeout: "float | None" = None) -> None:
     ``mcp_discovery_timeout`` in config) just caps the wait so a dead server
     can't freeze startup; servers that miss it are picked up by the automatic
     late-binding refresh.
+
+    When ``single_query`` is True, the bound comes from
+    ``mcp_single_query_discovery_timeout`` instead (default 15s vs 1.5s
+    interactive) because one-shot sessions have no second turn to recover.
     """
     thread = _mcp_discovery_thread
     if thread is None or not thread.is_alive():
         return
-    thread.join(timeout=_resolve_discovery_timeout(timeout))
+    thread.join(timeout=_resolve_discovery_timeout(timeout, single_query=single_query))
 
 
 def mcp_discovery_in_flight() -> bool:
@@ -192,3 +217,44 @@ def join_mcp_discovery(timeout: "float | None" = None) -> bool:
         return True
     thread.join(timeout=timeout)
     return not thread.is_alive()
+
+
+def ensure_mcp_discovery_before_agent_build(
+    *,
+    logger,
+    timeout: "float | None" = None,
+    single_query: bool = False,
+    thread_name: str = "cli-mcp-discovery",
+) -> None:
+    """Give configured MCP tools a bounded chance to register before AIAgent.
+
+    Non-interactive first turns (``chat -q``, ``hermes -z``) can construct
+    ``AIAgent`` before the normal banner or tool-list paths touch
+    ``get_tool_definitions()``.  Because the agent snapshots its tool
+    registry at construction time, the first and only model turn can miss
+    native ``mcp__...`` tools even when the MCP server is healthy.
+
+    ``wait_for_mcp_discovery()`` only joins an already-created discovery
+    thread, so it no-ops if a direct/single-query path reaches agent
+    construction before MCP startup created that thread.  This helper makes
+    the construction site self-sufficient: start discovery if needed, then
+    wait up to the configured bound.
+
+    When ``single_query`` is True, the larger
+    ``mcp_single_query_discovery_timeout`` bound is used (default 15s vs 1.5s
+    interactive) because one-shot sessions have no second turn to recover.
+
+    Failures are swallowed so a broken MCP config never aborts agent
+    construction — the agent runs without MCP tools, same as before.
+    """
+    try:
+        start_background_mcp_discovery(
+            logger=logger,
+            thread_name=thread_name,
+        )
+        wait_for_mcp_discovery(timeout=timeout, single_query=single_query)
+    except Exception:
+        logger.debug(
+            "MCP discovery readiness check failed before agent build",
+            exc_info=True,
+        )
diff --git a/hermes_cli/oneshot.py b/hermes_cli/oneshot.py
index 1f04173f0a6b7..f13fe64029d5c 100644
--- a/hermes_cli/oneshot.py
+++ b/hermes_cli/oneshot.py
@@ -395,6 +395,20 @@ def _run_agent(
     if toolsets_list is None and use_config_toolsets:
         toolsets_list = sorted(_get_platform_tools(cfg, "cli"))
 
+    # Ensure MCP tools are discovered before building the agent.  Oneshot
+    # bypasses cli.py's _prepare_agent_startup MCP background path and
+    # HermesCLI._init_agent's wait — it builds AIAgent directly here, so the
+    # tool snapshot at construction time misses any MCP server that hasn't
+    # registered yet.  This helper starts discovery if needed (idempotent) and
+    # bounded-waits with the larger single-query bound (default 15s) because
+    # there is only ONE turn and no between-turns late-binding refresh (#38448).
+    from hermes_cli.mcp_startup import ensure_mcp_discovery_before_agent_build
+
+    ensure_mcp_discovery_before_agent_build(
+        logger=logging.getLogger(__name__),
+        single_query=True,
+    )
+
     session_db = _create_session_db_for_oneshot()
     # The try spans agent construction (not just ``chat``) so the SQLite store
     # opened above is always closed — including when ``AIAgent(...)`` itself
diff --git a/tests/hermes_cli/test_mcp_discovery_timing.py b/tests/hermes_cli/test_mcp_discovery_timing.py
new file mode 100644
index 0000000000000..4660744f2c5b6
--- /dev/null
+++ b/tests/hermes_cli/test_mcp_discovery_timing.py
@@ -0,0 +1,310 @@
+"""Regression tests for MCP discovery timing in non-interactive sessions.
+
+Covers the race where AIAgent snapshots its tool registry at construction
+time before background MCP discovery finishes.  In single-query (``-q``) and
+oneshot (``-z``) mode there is only ONE turn — no between-turns late-binding
+refresh — so missing tools at construction are missing for the entire
+session.
+
+Tests verify:
+  1. The ``single_query`` flag resolves to the larger bound.
+  2. ``ensure_mcp_discovery_before_agent_build`` starts discovery if needed.
+  3. Oneshot calls the helper before AIAgent construction (ordering).
+  4. The wait stays bounded when discovery is slow (dead server).
+  5. Interactive mode keeps the small bound (not affected).
+"""
+
+from __future__ import annotations
+
+import sys
+import threading
+import time
+import types
+
+import pytest
+
+from hermes_cli import mcp_startup
+
+
+@pytest.fixture(autouse=True)
+def _reset_mcp_startup_state():
+    saved_started = mcp_startup._mcp_discovery_started
+    saved_thread = mcp_startup._mcp_discovery_thread
+    try:
+        mcp_startup._mcp_discovery_started = False
+        mcp_startup._mcp_discovery_thread = None
+        yield
+    finally:
+        thread = mcp_startup._mcp_discovery_thread
+        if thread is not None and thread.is_alive():
+            thread.join(timeout=1.0)
+        mcp_startup._mcp_discovery_started = saved_started
+        mcp_startup._mcp_discovery_thread = saved_thread
+
+
+# ── _resolve_discovery_timeout: single_query bound ──────────────────────────
+
+
+def test_resolve_discovery_timeout_single_query_uses_larger_bound(monkeypatch):
+    """Single-query mode reads the larger mcp_single_query_discovery_timeout."""
+    import hermes_cli.config as cfg
+
+    monkeypatch.setattr(
+        cfg,
+        "load_config",
+        lambda: {
+            "mcp_discovery_timeout": 1.5,
+            "mcp_single_query_discovery_timeout": 25.0,
+        },
+    )
+    assert mcp_startup._resolve_discovery_timeout(None) == 1.5
+    assert mcp_startup._resolve_discovery_timeout(None, single_query=True) == 25.0
+
+
+def test_resolve_discovery_timeout_single_query_falls_back(monkeypatch):
+    """Bad/absent single-query value falls back to DEFAULT_CONFIG, never hangs."""
+    import hermes_cli.config as cfg
+
+    default = float(cfg.DEFAULT_CONFIG.get("mcp_single_query_discovery_timeout", 15.0))
+    monkeypatch.setattr(
+        cfg, "load_config", lambda: {"mcp_single_query_discovery_timeout": 0}
+    )
+    assert mcp_startup._resolve_discovery_timeout(None, single_query=True) == default
+
+    monkeypatch.setattr(
+        cfg, "load_config", lambda: {"mcp_single_query_discovery_timeout": "oops"}
+    )
+    assert mcp_startup._resolve_discovery_timeout(None, single_query=True) == default
+
+    monkeypatch.setattr(cfg, "load_config", lambda: {})
+    assert mcp_startup._resolve_discovery_timeout(None, single_query=True) == default
+
+
+def test_resolve_discovery_timeout_explicit_overrides_single_query():
+    """An explicit timeout always wins, even in single-query mode."""
+    assert mcp_startup._resolve_discovery_timeout(5.0, single_query=True) == 5.0
+
+
+# ── ensure_mcp_discovery_before_agent_build ─────────────────────────────────
+
+
+def _stub_mcp_modules(monkeypatch):
+    """Stub MCP-related modules for helper tests."""
+    monkeypatch.setitem(
+        sys.modules,
+        "hermes_cli.config",
+        types.SimpleNamespace(
+            read_raw_config=lambda: {"mcp_servers": {"demo": {"transport": "stdio"}}},
+            load_config=lambda: {},
+            DEFAULT_CONFIG={"mcp_discovery_timeout": 0.1, "mcp_single_query_discovery_timeout": 0.2},
+        ),
+    )
+    monkeypatch.setitem(
+        sys.modules,
+        "tools.mcp_oauth",
+        types.SimpleNamespace(suppress_interactive_oauth=lambda: __import__("contextlib").nullcontext()),
+    )
+    monkeypatch.setitem(
+        sys.modules,
+        "tools.mcp_tool",
+        types.SimpleNamespace(
+            discover_mcp_tools=lambda: None,
+            get_mcp_status=lambda: [{"connected": True}],
+        ),
+    )
+
+
+def test_ensure_helper_starts_discovery_and_waits(monkeypatch):
+    """The helper starts background discovery if not yet started, then waits."""
+    _stub_mcp_modules(monkeypatch)
+    waited = []
+
+    original_wait = mcp_startup.wait_for_mcp_discovery
+
+    def _spy_wait(timeout=None, *, single_query=False):
+        waited.append(("wait", single_query))
+        original_wait(timeout=timeout, single_query=single_query)
+
+    monkeypatch.setattr(mcp_startup, "wait_for_mcp_discovery", _spy_wait)
+
+    logger = types.SimpleNamespace(debug=lambda *_a, **_k: None, warning=lambda *_a, **_k: None)
+
+    mcp_startup.ensure_mcp_discovery_before_agent_build(
+        logger=logger,
+        single_query=True,
+    )
+
+    # Discovery was started (thread created)
+    assert mcp_startup._mcp_discovery_thread is not None or waited
+    # Wait was called with single_query=True
+    assert any(call[1] is True for call in waited)
+
+
+def test_ensure_helper_is_idempotent(monkeypatch):
+    """Calling the helper twice doesn't start a second discovery thread."""
+    _stub_mcp_modules(monkeypatch)
+    logger = types.SimpleNamespace(debug=lambda *_a, **_k: None, warning=lambda *_a, **_k: None)
+
+    mcp_startup.ensure_mcp_discovery_before_agent_build(logger=logger)
+    thread1 = mcp_startup._mcp_discovery_thread
+    if thread1:
+        thread1.join(timeout=2.0)
+
+    mcp_startup.ensure_mcp_discovery_before_agent_build(logger=logger)
+    thread2 = mcp_startup._mcp_discovery_thread
+    if thread2:
+        thread2.join(timeout=2.0)
+
+    # Second call didn't create a new thread (first one completed, status shows connected)
+    # or if it did, it's because the first exited with zero connected — but we stubbed
+    # get_mcp_status to return connected=True, so no retry.
+    # The key invariant: no exception, no hang.
+
+
+def test_ensure_helper_swallows_errors(monkeypatch):
+    """A broken MCP config never aborts agent construction."""
+    monkeypatch.setitem(
+        sys.modules,
+        "hermes_cli.config",
+        types.SimpleNamespace(
+            read_raw_config=lambda: (_ for _ in ()).throw(RuntimeError("boom")),
+            load_config=lambda: {},
+            DEFAULT_CONFIG={},
+        ),
+    )
+    logger = types.SimpleNamespace(debug=lambda *_a, **_k: None, warning=lambda *_a, **_k: None)
+
+    # Should not raise
+    mcp_startup.ensure_mcp_discovery_before_agent_build(logger=logger)
+
+
+# ── oneshot ordering: discovery before AIAgent ──────────────────────────────
+
+
+def test_oneshot_calls_ensure_helper_before_aiagent(monkeypatch):
+    """oneshot._run_agent must call ensure_mcp_discovery_before_agent_build
+    before constructing AIAgent (#38448)."""
+    import inspect
+
+    import hermes_cli.oneshot as oneshot_mod
+
+    src = inspect.getsource(oneshot_mod._run_agent)
+    helper_idx = src.find("ensure_mcp_discovery_before_agent_build")
+    agent_idx = src.find("AIAgent(")
+    assert helper_idx != -1, "oneshot._run_agent must call ensure_mcp_discovery_before_agent_build"
+    assert agent_idx != -1, "oneshot._run_agent must construct AIAgent"
+    assert helper_idx < agent_idx, (
+        "ensure_mcp_discovery_before_agent_build must be called BEFORE AIAgent "
+        "construction in oneshot._run_agent (#38448)"
+    )
+
+
+# ── _init_agent ordering: discovery before AIAgent (CLI path) ───────────────
+
+
+def test_init_agent_calls_ensure_helper_before_aiagent(monkeypatch):
+    """cli_agent_setup_mixin._init_agent must call
+    ensure_mcp_discovery_before_agent_build before constructing AIAgent."""
+    import inspect
+
+    from hermes_cli.cli_agent_setup_mixin import CLIAgentSetupMixin
+
+    src = inspect.getsource(CLIAgentSetupMixin._init_agent)
+    helper_idx = src.find("ensure_mcp_discovery_before_agent_build")
+    # _init_agent delegates AIAgent construction to cli.py, so we check
+    # the helper appears before the session_db / agent construction logic
+    assert helper_idx != -1, (
+        "_init_agent must call ensure_mcp_discovery_before_agent_build"
+    )
+
+
+def test_init_agent_forwards_single_query_flag(monkeypatch):
+    """Single-query mode forwards single_query=True to the discovery wait."""
+    import cli as cli_mod
+
+    cli = cli_mod.HermesCLI(compact=True)
+    cli._session_db = object()
+    cli._resumed = False
+    cli.conversation_history = []
+    cli._install_tool_callbacks = lambda: None
+    cli._ensure_tirith_security = lambda: None
+    cli._ensure_runtime_credentials = lambda: True
+    cli._single_query_mode = True
+
+    seen = {}
+
+    def _fake_ensure(*, logger, timeout=None, single_query=False, **_kw):
+        seen["single_query"] = single_query
+
+    monkeypatch.setattr(
+        mcp_startup,
+        "ensure_mcp_discovery_before_agent_build",
+        _fake_ensure,
+    )
+    monkeypatch.setattr(cli_mod, "AIAgent", lambda *_a, **_k: types.SimpleNamespace())
+
+    assert cli._init_agent() is True
+    assert seen.get("single_query") is True
+
+
+def test_init_agent_defaults_to_interactive(monkeypatch):
+    """Without _single_query_mode, the helper uses interactive (short) bound."""
+    import cli as cli_mod
+
+    cli = cli_mod.HermesCLI(compact=True)
+    cli._session_db = object()
+    cli._resumed = False
+    cli.conversation_history = []
+    cli._install_tool_callbacks = lambda: None
+    cli._ensure_tirith_security = lambda: None
+    cli._ensure_runtime_credentials = lambda: True
+
+    seen = {}
+
+    def _fake_ensure(*, logger, timeout=None, single_query=False, **_kw):
+        seen["single_query"] = single_query
+
+    monkeypatch.setattr(
+        mcp_startup,
+        "ensure_mcp_discovery_before_agent_build",
+        _fake_ensure,
+    )
+    monkeypatch.setattr(cli_mod, "AIAgent", lambda *_a, **_k: types.SimpleNamespace())
+
+    assert cli._init_agent() is True
+    assert seen.get("single_query") is False
+
+
+# ── bounded wait: slow server doesn't freeze startup ────────────────────────
+
+
+def test_wait_stays_bounded_when_discovery_is_slow(monkeypatch):
+    """A slow/dead MCP server must not freeze startup: the wait is capped."""
+    import hermes_cli.config as cfg
+
+    monkeypatch.setattr(cfg, "load_config", lambda: {"mcp_single_query_discovery_timeout": 0.1})
+
+    stop = threading.Event()
+    thread = threading.Thread(target=lambda: stop.wait(10), daemon=True)
+    thread.start()
+    mcp_startup._mcp_discovery_thread = thread
+
+    try:
+        start = time.monotonic()
+        mcp_startup.wait_for_mcp_discovery(single_query=True)
+        elapsed = time.monotonic() - start
+    finally:
+        stop.set()
+
+    assert elapsed < 3.0, (
+        f"wait blocked {elapsed:.2f}s on a stuck MCP server — the wait must "
+        "stay bounded by mcp_single_query_discovery_timeout"
+    )
+
+
+def test_wait_returns_instantly_when_discovery_done():
+    """When discovery is already complete, the wait returns immediately."""
+    mcp_startup._mcp_discovery_thread = None
+    t0 = time.time()
+    mcp_startup.wait_for_mcp_discovery(single_query=True)
+    assert time.time() - t0 < 0.2