Seems unlikely to have a birdstrike shut off the transponder.
But we're having to think of every possibility.

I saw a report of an AD on the 777 describing corrosion around an antenna mounting that might lead to decompression.
Then got to thinking that if the transponder antenna mount were torn away the lack of antenna would look like loss of transponder to the ground stations.

Combine with sloppy flight deck behavior such that no pilot could get to his mask in time then you have the Payne Stewart scenario of a plane flying on autopilot with no live souls on board until it runs out of fuel.

But you'd expect one of the countries along the route to pick up the ghost plane on radar - so this theory has holes in it.

I think the high-probability one is hijacking followed by unauthorized pilot flying toward some target (like the high towers in Kuala Lumpur?) with a 911 type crash in mind.
But since this flight went out over water at night, perhaps they inadvertently descended into the water while still trying to figure out how to aim for their target?

I still find it a little amazing that in the "surveillance" world we seem to live in today, when the governments of the world know who we email, our friends on Facebook, and who we talk to on the phone that we can still manage to lose something the size of a 777.

The shock generated by the Boeing 777 mystery is largely a product of how much we’ve come to take for granted the modern superabundance of information. ..... If you log on to a flight-tracking website, you can punch in the flight number of any commercial aircraft and see its current location and direction. Seems pretty foolproof.
----------------snip-----------
Centers track each flight in a variety of ways. The first is with good old-fashioned radio calls. Controllers call up pilots to give them instructions, inquire about their intentions, and relay information. The second source of information is radar, of which there are two kinds. Primary radar tells operators where a plane is located. ......secondary radar, which pings an electronic device called a transponder inside each aircraft, which then transmits its altitude. Controllers will then be able to see on their screen the number of each flight, its location, and its altitude, derived from secondary radar.
---------------snip--------------
Together, these last two systems provide a robust and interlinking network, but they share the same limitation: They’re limited in range to somewhere between 100 to 200 miles from the nearest ground station, depending on atmospheric conditions. “In general, once you go far enough out over the water, if you don’t have a satellite link, there’s no way to talk to the ground,” says Rob Thomas,....

In such cases, the flight remains in the system, and controllers continue to see its symbol moving across their screens, based on the information obtained from the flight plan and from the last actual contact between controllers and the plane. .... They’re out of contact, and their status within the system is based on assumption until they can actually get back in contact and confirm that everything’s A-OK.

IIRC, and its been a while, is that RADAR isn't exactly hi-def, you simply see something vague which is why aircraft have transponders that reply with their ID. So if someone turns off that transponder the RADAR operators can't tell if its a plane or flock of birds or dense cloud0

Seems like they should make one transponder only accessible externally so they can't be turned off as I'm noticing that to be somewhat of a repeated theme in various hijackings and such.

The WSJ article has since been debunked.