barrel_owl
One of the million or so scenarios that have been offered is that there was an explosive decompression, which involved the elctronics bay and crew O2 area beneath the cabin floor and just aft of the cockpit.
Whatever happened rendered the radios and transponder, as well as the crew O2 inop. Apparently it did not affect the A/P.
The crew had a enough useful consciousness to get a bit of a descent and a return heading set, possibly to an FMS waypoint before passing out.
The plane descended to the preset altitude and went west.