Just caught up with the thread and the footage. Having looked at a lot of fake UFO videos (and knowing CGI), these are very interesting.
The most compelling parts for the FLIR footage being the turbulence the drone experiences, as well as the turbulence - either in the air between the drone and the aircraft, or vibration/general air turbulence from the drone itself. This amplifies the further the plane gets from the drone and the more the drone has to zoom in. You can see it as a slight shudder/blurring/recalibration of the image.
The orbs appear to follow this pattern too - although it's harder to see as they are smaller and moving.
So the FLIR drone footage and satellite footage of the plane looks genuine.
The only way to fake that would be with state of the art (for 2014) software (and hardware) designed to fake such videos (perhaps for training? Although that would be overkill), or would require intimate knowledge of either thousands of hours of real video footage or enough real world experience that you knew these tiny little details by eye.
TL:DR; all the (tiny, usually unnoticed) physics in the footage of the plane look genuine, detailed and how you would expect such footage to appear in real life.
As to the orbs - maybe they where added, but they also look mostly genuine (given how weird they are). The flash at the end also seems potentially genuine too. Even the trails they leave on the FLIR seems to add an element of reality to it - I've seen trails like that on other FLIR videos.
TLDR: something knocked out all communications, and the pilot tried in various ways to signal for help and to find an alternate place to land, but was unsuccessful.
On that note, given the plane in the drone footage causes turbulence to the drone - it may have deliberately passed in front of it, or close enough to get it's attention.
So this would potentially fit with the above, adding more weight to the idea this is real footage as the behavior fits what we know.