[BUG] Claude Desktop MCP tools stopped working - server connected, no errors, tools not available

Preflight Checklist

• [x] I have searched existing issues and this hasn't been reported yet
• [x] This is a single bug report (please file separate reports for different bugs)
• [x] I am using the latest version of Claude Code

What's Wrong?

Bug Description

MCP tools suddenly stopped working in Claude Desktop after days of successful use. Server initializes correctly, shows as connected, no error logs anywhere, but tools are not available to Claude in conversations.

Environment

• Claude Desktop (Windows)
• MCP Server: Custom FastMCP server with SSE transport
• Was working: Earlier today (Dec 19, 2025)
• Stopped working: ~3 hours ago, no changes made on my end

What I've verified

• MCP server is running and healthy
• Server shows successful initialization
• Connection shows as established in Claude Desktop
• No error logs on server or client side
• Zero changes to configuration or server code

Expected behavior

MCP tools should appear and be callable by Claude, as they were for several days prior.

Actual behavior

Server connects successfully but tools are not exposed to Claude. Claude responds without access to any MCP tools.

Notes

This matches the pattern from:

• Issue #2682 (tools not available despite successful connection)
• Issue #4188 (July 23, 2025 mass MCP breakage)
• November 16, 2025 SSE incident (Atlassian community thread)

40+ hours of development dependent on this integration. Nothing changed on my end.

What Should Happen?

MCP Tools should work

Error Messages/Logs

Steps to Reproduce

Ask Claude to run MCP tools

Claude Model

Opus

Is this a regression?

Yes, this worked in a previous version

Last Working Version

_No response_

Claude Code Version

Version 1.0.2339 (1782e2)

Platform

Anthropic API

Operating System

Windows

Terminal/Shell

PowerShell

Additional Information

_No response_