The captain and co-pilot tried to find the source of the smoke and fire. They switched off electrical "busses" to try to isolate it, in the process turning off systems like the transponder and ACARs automated update system (but not, presumably, the autopilot, which was flying the plane). They did not issue a distress call, because in a midair emergency your priorities are "aviate, navigate, communicate" — in that order. But smoke soon filled the cockpit and overwhelmed them (a tire fire could do this). The pilots passed out or died.
A pilot would know that we have oxygen masks in the cockpit...and the first course of action would be to put them on.