Describe the bug
Using the mongodb-mcp-server with gemini-3-pro-preview I chat a database query. Thinking shows the tool executes and returns a response, but gemini 400's the response and Goose outputs the following message:

Ran into this error: Request failed: Request failed with status: 400 Bad Request. Message: Function call is missing a thought_signature in functionCall parts. This is required for tools to work correctly, and missing thought_signature may lead to degraded model performance. Additional data, function call default_api:mongodb-mcp-server__find , position 2. Please refer to https://ai.google.dev/gemini-api/docs/thought-signatures for more details..Please retry if you think this is a transient or recoverable error.

That Google document reads, in part:

As a general rule, if you receive a thought signature in a model response, you should pass it back exactly as received when sending the conversation history in the next turn. When using Gemini 3 Pro, you must pass back thought signatures during function calling, otherwise you will get a validation error (4xx status code).

This works as expected if the model is gemini-2.5-pro

To Reproduce
Steps to reproduce the behavior:

1. Model gemini-3-pro-preview
2. Query mongodb database using mongodb-mcp-server
3. Tool call executes and returns results but Gemini 400's the response for missing thought signature.

Expected behavior
gemini-3-pro-preview should process the tool response

Screenshots
Goose messages gemini, gets tool call, processes tool call, obtains valid response.

Gemini 400's and Goose outputs the message indicated above in bug description. Full output of database query available but not shown in this report to save space.

Please provide the following information

• OS & Arch: Ubuntu 24.04.3 LTS
• Interface: UI
• Version: 1.13.1
• Extensions enabled: mongodb-mcp-server
• Provider & Model: Google – gemini-3-pro-preview]