Background Agent MCP Connections Destroyed After Text-Only Turn

[jorticus-msft]

Describe the bug

MCP tools in background agents (launched via the task tool) are unreliable. The CLI framework destroys MCP transport connections after any turn where the LLM produces a text-only response (no tool calls). This means background agents that depend on MCP tools intermittently fail with "Not connected" or "Connection closed" errors - even when the MCP server is healthy and reachable.

This is a blocking issue for using custom agents with MCP servers in background mode. Any non-trivial agent workflow that involves MCP tools will eventually hit this bug because the LLM occasionally produces a text-only response before making a tool call (~10% of the time with default prompts, 100% when the system prompt encourages reasoning before acting).

The bug does not affect standalone agent invocations (copilot --agent <agent> -p <prompt>) or the parent session's own MCP connections - only background agents.

Affected version

GitHub Copilot CLI 1.0.35

Steps to reproduce the behavior

Prerequisites

• Python 3.10+ with aiohttp (pip install aiohttp)

1. Add the attached server

from mcp.server.fastmcp import FastMCP

mcp = FastMCP("repro-mcp-server", port=8099)

@mcp.tool()
def fast_tool(query: str) -> str:
    """Returns immediately. Echoes the query back. For testing MCP transport reliability."""
    return f'{{"status": "ok", "query": "{query}"}}'

if __name__ == "__main__":
    mcp.run(transport="sse")

Save to ~/.copilot/repro_mcp_server.py

This is a minimal MCP SSE server that exposes a single fast_tool which immediately echoes back its input.

2. Create the agent definition

Save as ~/.copilot/agents/repro-test-agent.agent.md:

---
name: repro-test-agent
description: "Minimal agent for reproducing background-agent MCP bug."
mcp-servers:
  repro:
    type: sse
    url: "http://localhost:8099/sse"
    tools: ["*"]
tools: ['repro/*']
---

You are a test agent with a STRICT protocol. You MUST follow this exact sequence
for EVERY request:

Turn 1: Reply with ONLY this exact text: "Processing request." — absolutely NO
tool calls on this turn.
Turn 2: Now call the requested tool.

CRITICAL RULE: You are FORBIDDEN from calling any tool on your first turn. Your
first message MUST be pure text with zero tool calls.

The system prompt forces a text-only first turn. This simulates the natural LLM behaviour of reasoning before acting, which triggers the bug deterministically.

When run, the background agent produces "Processing request." on turn 1, calls repro-fast_tool on turn 2, and returns {"status": "ok", "query": "test-bug"}.

Expected behavior

I expect that MCP tool calling is reliable for any background agent session.

What actually happens

The agent produces text on turn 1. The framework fires internal response and messages_snapshot events which tear down the MCP transport. The agent either never gets a turn 2, or turn 2's tool call fails on a dead connection.

Debug log signature (~/.copilot/logs/process-*.log):

[DEBUG] response (Request-ID null):
[DEBUG] Ignoring event of kind: response
[DEBUG] Ignoring event of kind: messages_snapshot
[ERROR] MCP transport for repro closed
[ERROR] MCP client for repro closed

Repro rate: 3/3 (100%) with the included agent definition.

Intermittent variant without special system prompt

The "text first" system prompt makes the bug deterministic, but it also occurs naturally. With a neutral system prompt ("call the tool and report the result"), the LLM occasionally produces text before a tool call. In testing:

• 2 failures out of ~20 background agent invocations with neutral prompts (~10%)

Non-background agents are not affected

• copilot --agent <agent> -p <prompt> (standalone mode): MCP survives across turns. 0/15 failures.
• Parent session MCP tools: text-only turns do not destroy connections.
• The bug is specific to background agents spawned via the task tool.

Additional context

CLI log: standalone agent (works — MCP survives)

copilot --agent repro-test-agent -p 'Call repro-fast_tool with query "standalone-test".' --allow-all-tools

09:24:25.374 [ERROR] Starting remote MCP client for repro with url: http://localhost:8099/sse
09:24:25.402 [ERROR] MCP client for repro connected, took 27ms
09:24:25.533 [DEBUG] Adding tool: repro-fast_tool
09:24:27.996 [DEBUG] Making Anthropic Messages streaming request with messages: [
09:24:32.836 [DEBUG] response (Request-ID null):        ← LLM response arrives
09:24:40.914 [DEBUG] Tool calls count: 2                ← includes tool_use
09:24:40.915 [DEBUG] Permission request (kind=mcp)      ← tool executes
09:24:40.971 [DEBUG] Tool invocation result: {"result":"{\"status\": \"ok\", \"query\": \"standalone-test\"}"}
09:24:40.997 [DEBUG] Making Anthropic Messages streaming request  ← turn 2 (report result)
09:24:43.433 [DEBUG] response (Request-ID null):
09:24:43.434 [DEBUG] Ignoring event of kind: response             ← event fires...
09:24:43.434 [DEBUG] Ignoring event of kind: messages_snapshot
                                                                   ← but NO MCP teardown

CLI log: background agent (fails — MCP destroyed)

copilot -p '...launch background agent...' --allow-all-tools

09:19:17.426 [INFO]  Started background agent with id: bug-repro
09:19:17.486 [INFO]  Custom agent "repro-test-agent" invoked
09:19:17.545 [ERROR] Starting remote MCP client for repro with url: http://localhost:8099/sse
09:19:17.573 [ERROR] MCP client for repro connected, took 27ms
09:19:17.664 [DEBUG] Adding tool: repro-fast_tool
09:19:17.666 [INFO]  Found 1 MCP tools from server 'repro'
09:19:17.671 [INFO]  Custom agent "repro-test-agent" using tools: repro-fast_tool, view
09:19:18.074 [DEBUG] Making Anthropic Messages streaming request  ← child agent turn 1
09:19:20.632 [DEBUG] response (Request-ID null):        ← text-only "Processing request."
                                                         (no "Tool calls count" line)
09:19:20.715 [INFO]  System notification: Agent "bug-repro" has finished processing
                                                         ← agent treated as DONE after text-only turn
...
09:19:54.619 [DEBUG] response (Request-ID null):
09:19:54.621 [DEBUG] Ignoring event of kind: response             ← same event as standalone...
09:19:54.623 [DEBUG] Ignoring event of kind: messages_snapshot
09:19:54.629 [ERROR] MCP transport for repro closed               ← ...but HERE it kills MCP
09:19:54.629 [ERROR] MCP client for repro closed

Note: both modes fire Ignoring event of kind: response, but only the background agent path destroys the MCP transport afterward.