[BUG] Plugin MCP tools (bio-research, etc.) return "Session not found" error - plugins work on Claude.ai Cowork but not in Claude Code

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?

Plugin MCP tools (PubMed, ChEMBL, bioRxiv, ClinicalTrials from bio-research plugin) are registered as deferred tools but fail with "Session not found" when called. The same plugins work perfectly on Claude.ai Cowork. Plugin skills and agents load fine — only the MCP tool layer is broken.

In VSCode: ToolSearch finds the tools, but calling them returns:
"Session not found: Session ID does not exist. Please initialize a new session first."

In Terminal CLI: The tools don't exist at all — Claude falls back to Web Search instead.

The /mcp command shows 50 MCP servers but bio-research MCP servers don't appear in the list at all.

What Should Happen?

Plugin MCP tools should initialize their sessions automatically when Claude Code starts, just as they do on Claude.ai Cowork. When I ask "Search PubMed for COVID-19 mRNA vaccine papers", Claude Code should use the mcp__plugin_bio-research_pubmed__search_articles tool — not fall back to Web Search.

Error Messages/Logs

Streamable HTTP error: Error POSTing to endpoint: {"error":"Session not found","message":"Session ID '436be88b-bcae-4e88-9361-f9a5d34acf2b' does not exist. Please initialize a new session first."}

Steps to Reproduce

1. Install the bio-research plugin from the marketplace (/plugins)
2. Confirm it appears in ~/.claude/plugins/installed_plugins.json and is enabled in settings.json
3. Start a new Claude Code session (VSCode or terminal claude)
4. Run /status → shows "34 need auth, 3 pending, 13 failed" for MCP servers
5. Run /mcp → bio-research MCP servers do NOT appear in the list
6. In VSCode, use ToolSearch to find mcp__plugin_bio-research_pubmed__search_articles → tool IS found as deferred tool
7. Call the tool → fails with "Session not found" error
8. In terminal CLI, ask to search PubMed → Claude uses Web Search instead of plugin MCP tool
9. Restart terminal (exit → claude) → same result
10. /reload-plugins → loads 18 plugins but MCP sessions still fail

Claude Model

Opus

Is this a regression?

I don't know

Last Working Version

2.1.86

Claude Code Version

Claude Max 2.1.86

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

Key Finding: Works on Claude.ai Cowork, Broken on Claude Code

| Environment | Plugin Skills/Agents | Plugin MCP Tools |
|-------------|---------------------|-----------------|
| Claude.ai Cowork | ✅ Works | ✅ Works |
| Claude Code VSCode | ✅ Works (11 skills, 10 agents) | ❌ "Session not found" |
| Claude Code Terminal | ✅ Works | ❌ Tools don't exist |

What I've Tried

• Restarting Claude Code (terminal and VSCode)
• /reload-plugins (loads plugins but MCP sessions still fail)
• Verified network connectivity (curl to Anthropic API works)
• Confirmed all 19 plugins enabled in settings.json

Impact

Claude Code users handle the most complex workflows but cannot use plugin MCP tools at all. This forces context-switching to Claude.ai Cowork for any plugin-dependent task (PubMed searches, ChEMBL queries, ClinicalTrials lookups, etc.).

Related Issues

• #9608 (Session not found → should create new session)
• #11175 (MCP tools not available despite loading)
• #35452 (MCP server initialization failures)

Suggested Fix

When a deferred plugin MCP tool is called and the session doesn't exist, Claude Code should automatically initialize a new MCP session rather than returning a fatal error.