Went to do some research after @niels nielsen's answer; the engine being used on the MQ-9 is the Honeywell TPE331-10. As Niels has rightly pointed out, the turboprop engine has its inlet facing the rear, and the turbine exhaust faces forward (I believe this is known as reverse flow).
Screen grabs from the Youtube video below. The left image depicts the aft section in off-white (gold flanges are to the prop driveshaft), with the intake below. The right image depicts the turbine exhaust, which faces forward.
Now to answer the question: inferring from this Alamy stock photo, the splitter for the main scoop diverts the airflow into two channels for the main engine intake (the two red kidney-shaped covers). The NACA duct along the centreline is for a separate cooler (the rectangular opening).
Additional photos also show how the air is routed around the engine. The left picture shows a duct that likely comes from the port air channel, which is connected to a plenum(?). The right picture shows a clearer internal view, without the duct. The duct exits are circled in yellow. I am guessing this is the same on the starboard side.
From the information that I could find, this is my guess on how the internal ducting is done. Please excuse the crudely annotated screenshot: