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Symptom
You added the Atlassian Jira (Rovo) MCP server to Fleet and the server connects successfully, but no tools load — the tools list comes back empty.
Most common cause: the deprecated SSE endpoint
In most cases this is an endpoint issue, not a Fleet bug. If the server URL ends in /v1/sse, that is Atlassian's deprecated HTTP+SSE endpoint. Atlassian is retiring it, and MCP clients should use the newer Streamable HTTP endpoint instead.
Fix: Switch the URL to Atlassian's recommended endpoint:
https://mcp.atlassian.com/v1/mcp/authv2
Because Fleet stores tool references by MCP server URL, changing the URL on an existing entry will break agents that use those tools. Delete the existing Jira server entry and re-add it with the new URL rather than editing it in place. (If you edit in place instead, remove the affected tools from each agent and re-add them so they reference the new URL.)
Per Atlassian, the SSE endpoint (https://mcp.atlassian.com/v1/sse) will no longer be supported after 30 June 2026, so the Streamable HTTP endpoint is the correct choice going forward.
If tools are still empty
Work through these in order:
Check for duplicate entries. Confirm there is only one Jira MCP server entry on the MCP Servers page. Duplicate rows for the same service have been observed to cause tools to return empty.
Verify authentication. The Auth type in Fleet should be OAuth 2.1 (Auto), and the browser consent flow must be completed. The Atlassian MCP server uses OAuth 2.1 as its primary method. API-token auth is only available if the Atlassian admin has enabled it; if the admin has disabled it, clients must use OAuth 2.1.
Confirm first-time authorization. The Atlassian MCP app is installed the first time a user completes the OAuth (3LO) consent flow for the site. That first user needs access to the Atlassian products the MCP scopes request (e.g., Jira). If no one has completed consent, users may see an authorization error.
Check IP allowlisting. Fleet performs tool discovery server-side (it fetches the tool list from the MCP server, not from the browser). If your organization enforces IP allowlisting on Atlassian Cloud, tool calls through the Rovo MCP server must come from an allowed IP — so a blocked address can result in an empty tool list.
Capture a trace. If tools are still empty, grab a failing trace ID in Fleet (right-click the run → view trace) and share it with LangChain support for further diagnosis.
Resolution
Once the URL is on the Streamable HTTP endpoint and OAuth is connected, Fleet discovers the Jira tools automatically. In practice, switching from the SSE endpoint to the Streamable HTTP endpoint resolves most "tools not loading" cases.