How does a single user query flow through an MCP-enabled application?

Let's trace a complete example. A user asks what repositories do I have. First, your server receives the query and needs to know what tools are available, so it asks the MCP client for them. The MCP client sends a list tools request to the MCP server and receives a list tools result. Your server then sends the user's query plus the available tools to Claude. Claude decides it needs to call a tool, so your server asks the MCP client to run it. The client sends a call tool request, the MCP server makes the actual GitHub API call, and the result flows back as a call tool result. Finally, your server sends the tool results back to Claude, who formulates the answer for the user.