The document discusses two ways to stop a Mule flow after processing a file: 1) stopping the flow at the end using a Groovy component, or 2) stopping the connector at the end. It focuses on the first option, showing how a Groovy script can call muleContext.registry.lookupFlowConstruct('Flow name').stop() to end the flow after a file has been read. This prevents any additional files from being processed by the inbound endpoint.