The Flat Files are received by an BizTalk adapter
associated to a receive location
A pipeline organized in the receive location will be dependable for transforming the Flat File into its equivalent XML,
An orchestration will subscribe to the XML document and this message will go through the business process. While there is no need to have orchestrations in a pure messaging scenario.
BizTalk can send XML messages again as a Flat Files by using another pipeline in the send ports If and when it is necessary, which will be responsible for transforming the XML into its equivalent the Flat File.