The folks over at airliners.net have pointed out that the 777's collision avoidance system only works if both planes' transponders are turned on. That doesn't mean this scenario is impossible, but it does raise the level of sophistication required. Sadly, I feel like whatever happened, the amount of sophistication involved increasingly points toward the involvement of one or more state actors. If that's the case, I'm…
Now what could cause that - perhaps a good mystery. Everyone likes a good mystery.
Baikonur is a pretty f'ing good place to hide something like a 777, and is very proximal to the last possible position. Been there. Middle of nowhere. Airstrip is high security, remote, and has underground hangers. Local populace are very well versed in "I see nothing". It's also jurisdictionally weird, being a bit of Kaz rented to Russia as sovereign territory, meaning that any legal search would be very tricky to arrange to say the least.
Add that to the big old pile of theories.