diff --git a/docs/integrations/mcp.mdx b/docs/integrations/mcp.mdx
index d2acca18..c80e2f78 100644
--- a/docs/integrations/mcp.mdx
+++ b/docs/integrations/mcp.mdx
@@ -71,6 +71,27 @@ Strix reads this file at the start of each run. There is no default file, so no
   server offers, or set it to a list of tool names to allow only those.
 </ParamField>
 
+<ParamField path="notes" type="string">
+  Free-text notes for the agent about what this connection is and how you want
+  it used, for example "Staging analytics database, read-only, prefer aggregate
+  queries." When set, the notes are given to the agent at the start of the run
+  as a description of the connection.
+</ParamField>
+
+## Choosing connections per run
+
+By default every connection in the file is used on each run. To narrow it for a
+single run without editing the file, use either flag (both repeatable):
+
+```bash
+strix --mcp-server github -t ...        # use only the named connection(s)
+strix --mcp-exclude staging-db -t ...   # use everything except the named one(s)
+```
+
+`--mcp-server` keeps only the connections you name; `--mcp-exclude` drops the
+ones you name. Connection names must be unique in the file; if two entries share
+a name, the first is kept and the rest are ignored.
+
 ## Pointing at a different file
 
 To read the config from another path instead of `~/.strix/mcp-servers.json`, either pass `--mcp-config <path>` on the command line:
diff --git a/strix/core/runner.py b/strix/core/runner.py
index 9dee9779..e90360f1 100644
--- a/strix/core/runner.py
+++ b/strix/core/runner.py
@@ -74,6 +74,23 @@ def _mcp_startup_summary(connections: list[ConnectedMcpServer]) -> str:
     return f"MCP: connected {server_count} {servers_word} ({tool_count} {tools_word}): {names}"
 
 
+def _mcp_connection_notes(connections: list[ConnectedMcpServer]) -> str | None:
+    """A block describing the connections the user left notes on, for the agent.
+
+    Only connections with notes are listed, so the note describes the connection
+    once rather than being repeated onto every tool. Returns ``None`` when no
+    connection has notes.
+    """
+    noted = [(c.name, c.notes) for c in connections if c.notes]
+    if not noted:
+        return None
+    lines = "\n".join(f"- `{name}.*` tools: {notes}" for name, notes in noted)
+    return (
+        "The user connected these MCP servers for this run and left notes on how "
+        f"to use each:\n{lines}"
+    )
+
+
 def _merge_root_prompt_context(
     scope_context: dict[str, Any],
     extra_system_prompt_context: dict[str, Any] | None,
@@ -323,6 +340,9 @@ async def run_strix_scan(
                 mcp_servers = [c.server for c in connections]
                 if connections:
                     report(_mcp_startup_summary(connections))
+                    notes_block = _mcp_connection_notes(connections)
+                    if notes_block:
+                        root_task = f"{root_task}\n\n{notes_block}"
         except Exception:
             logger.exception("Failed to connect user MCP servers; continuing without them")
 
diff --git a/strix/interface/cli_args.py b/strix/interface/cli_args.py
index 248bcb70..5b789eda 100644
--- a/strix/interface/cli_args.py
+++ b/strix/interface/cli_args.py
@@ -227,6 +227,23 @@ Examples:
         help="Path to an MCP servers JSON file to use instead of ~/.strix/mcp-servers.json.",
     )
 
+    parser.add_argument(
+        "--mcp-server",
+        dest="mcp_server",
+        action="append",
+        metavar="NAME",
+        help="Use only this MCP connection for the run, by its config name "
+        "(repeatable). Every other configured connection is skipped.",
+    )
+
+    parser.add_argument(
+        "--mcp-exclude",
+        dest="mcp_exclude",
+        action="append",
+        metavar="NAME",
+        help="Skip this MCP connection for the run, by its config name (repeatable).",
+    )
+
     parser.add_argument(
         "--max-budget",
         "--max-budget-usd",
@@ -283,6 +300,12 @@ Examples:
         # setting it here makes the flag win over the default location.
         os.environ["STRIX_MCP_CONFIG"] = str(mcp_config_path)
 
+    # The MCP loader reads these as its per-run include/exclude selection.
+    if args.mcp_server:
+        os.environ["STRIX_MCP_ONLY"] = ",".join(args.mcp_server)
+    if args.mcp_exclude:
+        os.environ["STRIX_MCP_EXCLUDE"] = ",".join(args.mcp_exclude)
+
     if args.update:
         sys.exit(0 if self_update() else 1)
 
diff --git a/strix/tools/mcp/client.py b/strix/tools/mcp/client.py
index 83aa93f4..7f79fb9f 100644
--- a/strix/tools/mcp/client.py
+++ b/strix/tools/mcp/client.py
@@ -13,6 +13,7 @@ and skipped, so one bad connection never fails the run.
 
 from __future__ import annotations
 
+import contextlib
 import json
 import logging
 from typing import TYPE_CHECKING, Any, NamedTuple, cast
@@ -54,12 +55,15 @@ class ConnectedMcpServer(NamedTuple):
     """One successfully connected MCP server and how many tools it registered.
 
     ``server`` is kept so the caller can clean it up when the run ends;
-    ``name`` and ``tool_count`` let the caller show the user a startup summary.
+    ``name`` and ``tool_count`` let the caller show the user a startup summary;
+    ``notes`` carries the connection's optional free-text description so the
+    caller can surface it to the agent as context about the connection.
     """
 
     server: MCPServer
     name: str
     tool_count: int
+    notes: str | None = None
 
 
 def _auth_headers(config: McpConnectionConfig) -> dict[str, str]:
@@ -235,12 +239,28 @@ async def connect_mcp_servers(
         except Exception:
             logger.exception("Skipping MCP connection %r", config.name)
             if server is not None:
-                await server.cleanup()  # type: ignore[no-untyped-call]
+                with contextlib.suppress(Exception):
+                    await server.cleanup()  # type: ignore[no-untyped-call]
             continue
+        except BaseException:
+            # A cancellation (or other non-Exception failure) mid-connect must not
+            # orphan MCP subprocesses or HTTP sessions. Clean up the server being
+            # connected and every server already connected, then re-raise so the
+            # caller still stops. The runner only receives the list on a clean
+            # return, so on an abnormal exit this function owns the cleanup.
+            if server is not None:
+                with contextlib.suppress(Exception):
+                    await server.cleanup()  # type: ignore[no-untyped-call]
+            for established in connected:
+                with contextlib.suppress(Exception):
+                    await established.server.cleanup()  # type: ignore[no-untyped-call]
+            raise
 
         logger.info("Connected MCP server %r (%d tools)", config.name, len(tools))
         connected.append(
-            ConnectedMcpServer(server=server, name=config.name, tool_count=len(tools))
+            ConnectedMcpServer(
+                server=server, name=config.name, tool_count=len(tools), notes=config.notes
+            )
         )
 
     return connected
diff --git a/strix/tools/mcp/config.py b/strix/tools/mcp/config.py
index 15acbeaa..8df59ac2 100644
--- a/strix/tools/mcp/config.py
+++ b/strix/tools/mcp/config.py
@@ -59,6 +59,11 @@ class McpConnectionConfig(BaseModel):
     """Tool allowlist, applied after the server lists its tools. ``None`` (the
     default) exposes every tool the server lists; a list restricts to it."""
 
+    notes: str | None = None
+    """Free-text notes for the agent describing what this connection is and how
+    to use it. When set, they are prefixed onto each of the connection's tool
+    descriptions so the agent sees them."""
+
     @model_validator(mode="after")
     def _check_transport_fields(self) -> McpConnectionConfig:
         if self.transport == "http" and not self.url:
diff --git a/strix/tools/mcp/loader.py b/strix/tools/mcp/loader.py
index fa7ccb17..c179981d 100644
--- a/strix/tools/mcp/loader.py
+++ b/strix/tools/mcp/loader.py
@@ -28,6 +28,10 @@ logger = logging.getLogger(__name__)
 
 _DEFAULT_PATH: Path = Path.home() / ".strix" / "mcp-servers.json"
 _PATH_ENV_VAR = "STRIX_MCP_CONFIG"
+# Per-run selection, set by the --mcp-server / --mcp-exclude CLI flags. Each is a
+# comma-separated list of connection names.
+_ONLY_ENV_VAR = "STRIX_MCP_ONLY"
+_EXCLUDE_ENV_VAR = "STRIX_MCP_EXCLUDE"
 
 
 def _resolve_path(path: Path | None) -> Path:
@@ -39,6 +43,60 @@ def _resolve_path(path: Path | None) -> Path:
     return _DEFAULT_PATH
 
 
+def _dedupe_by_name(configs: list[McpConnectionConfig]) -> list[McpConnectionConfig]:
+    """Keep the first connection of each name, dropping later duplicates.
+
+    Names namespace a server's tools (``<name>.<tool>``), so two connections
+    sharing a name would collide and the second's tools would be silently
+    rejected at registration. Drop the duplicate here, with a warning, instead.
+    """
+    seen: set[str] = set()
+    unique: list[McpConnectionConfig] = []
+    for config in configs:
+        if config.name in seen:
+            logger.warning(
+                "Ignoring MCP server %r: another connection already uses that name "
+                "(names must be unique because they namespace the server's tools).",
+                config.name,
+            )
+            continue
+        seen.add(config.name)
+        unique.append(config)
+    return unique
+
+
+def _parse_names(env_var: str) -> set[str]:
+    return {name.strip() for name in os.environ.get(env_var, "").split(",") if name.strip()}
+
+
+def _apply_run_selection(configs: list[McpConnectionConfig]) -> list[McpConnectionConfig]:
+    """Restrict this run's connections to an optional include/exclude selection.
+
+    ``STRIX_MCP_ONLY`` (if set) keeps only the named connections; then
+    ``STRIX_MCP_EXCLUDE`` drops any named connection. With neither set, every
+    connection is kept.
+    """
+    only = _parse_names(_ONLY_ENV_VAR)
+    exclude = _parse_names(_EXCLUDE_ENV_VAR)
+    if not only and not exclude:
+        return configs
+
+    available = {config.name for config in configs}
+    for name in sorted((only | exclude) - available):
+        logger.warning(
+            "MCP connection selection named %r, which is not configured; ignoring it", name
+        )
+
+    selected: list[McpConnectionConfig] = []
+    for config in configs:
+        if only and config.name not in only:
+            continue
+        if config.name in exclude:
+            continue
+        selected.append(config)
+    return selected
+
+
 def load_user_mcp_configs(path: Path | None = None) -> list[McpConnectionConfig]:
     """Load MCP connection configs from the user's JSON file.
 
@@ -46,7 +104,8 @@ def load_user_mcp_configs(path: Path | None = None) -> list[McpConnectionConfig]
     ``~/.strix/mcp-servers.json``. The file is a JSON list of server entries.
     A missing file returns ``[]``; an unreadable or non-list file is logged and
     returns ``[]``; individual entries that fail validation are logged and
-    skipped.
+    skipped. Connections sharing a name are de-duplicated (first wins), and an
+    optional per-run include/exclude selection is applied last.
     """
     source = _resolve_path(path)
     if not source.exists():
@@ -70,4 +129,4 @@ def load_user_mcp_configs(path: Path | None = None) -> list[McpConnectionConfig]
         except ValidationError as exc:
             logger.warning("Skipping invalid MCP server entry #%d in %s: %s", index, source, exc)
 
-    return configs
+    return _apply_run_selection(_dedupe_by_name(configs))
diff --git a/tests/test_cli_mcp_config.py b/tests/test_cli_mcp_config.py
index 12de41d4..a63f6efe 100644
--- a/tests/test_cli_mcp_config.py
+++ b/tests/test_cli_mcp_config.py
@@ -59,3 +59,30 @@ def test_mcp_config_flag_rejects_missing_file(
         cli_main.parse_arguments()
 
     assert "--mcp-config file not found" in capsys.readouterr().err
+
+
+def test_mcp_server_flags_set_selection_env(monkeypatch: pytest.MonkeyPatch) -> None:
+    _stub_settings(monkeypatch)
+    monkeypatch.delenv("STRIX_MCP_ONLY", raising=False)
+    monkeypatch.delenv("STRIX_MCP_EXCLUDE", raising=False)
+    monkeypatch.setattr(
+        sys,
+        "argv",
+        [
+            "strix",
+            "-t",
+            "https://test.com/",
+            "-n",
+            "--mcp-server",
+            "a",
+            "--mcp-server",
+            "b",
+            "--mcp-exclude",
+            "c",
+        ],
+    )
+
+    cli_main.parse_arguments()
+
+    assert os.environ["STRIX_MCP_ONLY"] == "a,b"
+    assert os.environ["STRIX_MCP_EXCLUDE"] == "c"
diff --git a/tests/test_mcp_client.py b/tests/test_mcp_client.py
index 19f66426..3a7386e7 100644
--- a/tests/test_mcp_client.py
+++ b/tests/test_mcp_client.py
@@ -2,6 +2,7 @@
 
 from __future__ import annotations
 
+import asyncio
 import json
 from typing import TYPE_CHECKING, Any
 
@@ -12,11 +13,14 @@ from mcp.types import Tool as MCPTool
 from pydantic import ValidationError
 
 from strix.agents import factory
+from strix.core.runner import _mcp_connection_notes
 from strix.tools.mcp import (
     BearerAuth,
+    ConnectedMcpServer,
     McpConnectionConfig,
     load_user_mcp_configs,
 )
+from strix.tools.mcp import client as mcp_client
 from strix.tools.mcp.client import _auth_headers, _build_server, _register_server_tools
 
 
@@ -438,3 +442,141 @@ def test_loader_reads_env_var_override(tmp_path: Path, monkeypatch: pytest.Monke
     configs = load_user_mcp_configs()
 
     assert [c.name for c in configs] == ["local_fs"]
+
+
+# --- connection notes --------------------------------------------------------
+
+
+@pytest.mark.asyncio
+async def test_connection_notes_are_carried_on_the_connection(
+    monkeypatch: pytest.MonkeyPatch,
+) -> None:
+    server = FakeMCPServer("db", [_mcp_tool("query")])
+    monkeypatch.setattr(mcp_client, "_build_server", lambda _config: server)
+    config = McpConnectionConfig(
+        name="db",
+        url="https://mcp.example.com",
+        notes="Staging analytics DB; read-only.",
+        allowed_tools=["query"],
+    )
+
+    connections = await mcp_client.connect_mcp_servers([config])
+
+    # Notes ride on the connection (surfaced once), not stapled onto each tool.
+    assert connections[0].notes == "Staging analytics DB; read-only."
+
+
+def test_connection_notes_block_lists_only_noted_connections() -> None:
+    connections = [
+        ConnectedMcpServer(
+            server=FakeMCPServer("db", []), name="db", tool_count=2, notes="staging, read-only"
+        ),
+        ConnectedMcpServer(server=FakeMCPServer("fs", []), name="fs", tool_count=1, notes=None),
+    ]
+
+    block = _mcp_connection_notes(connections)
+
+    assert block is not None
+    assert "db" in block
+    assert "staging, read-only" in block
+    # A connection without notes is not listed.
+    assert "fs" not in block
+
+
+def test_connection_notes_block_is_none_without_notes() -> None:
+    connections = [
+        ConnectedMcpServer(server=FakeMCPServer("db", []), name="db", tool_count=1, notes=None)
+    ]
+
+    assert _mcp_connection_notes(connections) is None
+
+
+# --- cancellation cleanup ----------------------------------------------------
+
+
+@pytest.mark.asyncio
+async def test_connect_cleans_up_when_cancelled_mid_connect(
+    monkeypatch: pytest.MonkeyPatch,
+) -> None:
+    cleaned: list[str] = []
+
+    class _Tracking(FakeMCPServer):
+        def __init__(self, name: str, *, fail_connect: bool = False) -> None:
+            super().__init__(name, [_mcp_tool("t")])
+            self._fail_connect = fail_connect
+
+        async def connect(self) -> None:
+            if self._fail_connect:
+                raise asyncio.CancelledError
+
+        async def cleanup(self) -> None:
+            cleaned.append(self._name)
+
+    servers = {"good": _Tracking("good"), "bad": _Tracking("bad", fail_connect=True)}
+    monkeypatch.setattr(mcp_client, "_build_server", lambda config: servers[config.name])
+
+    configs = [
+        McpConnectionConfig(name="good", url="https://mcp.example.com", allowed_tools=["t"]),
+        McpConnectionConfig(name="bad", url="https://mcp.example.com", allowed_tools=["t"]),
+    ]
+
+    with pytest.raises(asyncio.CancelledError):
+        await mcp_client.connect_mcp_servers(configs)
+
+    # The server being connected when cancelled, and the one already connected,
+    # are both cleaned up rather than orphaned.
+    assert cleaned == ["bad", "good"]
+
+
+# --- duplicate names and run selection ---------------------------------------
+
+
+def _names_file(tmp_path: Path, *names: str) -> Path:
+    config_file = tmp_path / "mcp-servers.json"
+    config_file.write_text(
+        json.dumps([{"name": n, "transport": "stdio", "command": "npx"} for n in names]),
+        encoding="utf-8",
+    )
+    return config_file
+
+
+def test_loader_drops_duplicate_named_connections(tmp_path: Path) -> None:
+    config_file = tmp_path / "mcp-servers.json"
+    config_file.write_text(
+        json.dumps(
+            [
+                {"name": "dup", "transport": "stdio", "command": "first"},
+                {"name": "dup", "transport": "stdio", "command": "second"},
+                {"name": "other", "transport": "stdio", "command": "npx"},
+            ]
+        ),
+        encoding="utf-8",
+    )
+
+    configs = load_user_mcp_configs(config_file)
+
+    # Duplicate name is dropped; the first entry wins.
+    assert [c.name for c in configs] == ["dup", "other"]
+    assert configs[0].command == "first"
+
+
+def test_loader_include_selection_keeps_only_named(
+    tmp_path: Path, monkeypatch: pytest.MonkeyPatch
+) -> None:
+    config_file = _names_file(tmp_path, "a", "b", "c")
+    monkeypatch.setenv("STRIX_MCP_ONLY", "a,c")
+
+    configs = load_user_mcp_configs(config_file)
+
+    assert [c.name for c in configs] == ["a", "c"]
+
+
+def test_loader_exclude_selection_drops_named(
+    tmp_path: Path, monkeypatch: pytest.MonkeyPatch
+) -> None:
+    config_file = _names_file(tmp_path, "a", "b", "c")
+    monkeypatch.setenv("STRIX_MCP_EXCLUDE", "b")
+
+    configs = load_user_mcp_configs(config_file)
+
+    assert [c.name for c in configs] == ["a", "c"]