Things were bad at home with one of the two pilots --he was losing his spouse and his kids. Maybe he also has some professional problems with the airline --impending job loss?
He kills the other pilot, then depressurizes the plane to knock out all the passengers. He briefly hears a banging on the cockpit door, but it subsides after 1 minute, then stops totally: the widely-imagined battle royal for survival by the passengers is a non-event. He shuts down both transponders and all comms.
He flies on, on oxygen, contemplating his life, the passengers meanwhile dying from oxygen deprivation. He turns the plane dramatically, beginning a suicidal dive, plunging 40,000 feet in just one minute, only to chicken out.
He flies on for hours, silently trying to summon up the courage to end it all. His indecision is overtaken by his fuel situation, and on vapors he finally slams into the ocean, knocking himself out and dying.
Scenario 2: Hijack
The two Lothario pilots invite the 2 most attractive women on the plane into the cockpit, the better to impress them with their studly technical skill. This habit of theirs had been previously noted by other more radical passengers and quietly passed up the command chain, who dispatched comely young women to "coincidentally" fly in their plane.
During their cockpit party the pilots are overcome by a sedative secreted into their drinks. The women unlock the cockpit door, later accessed by a completely calm and properly trained hijack pilot clicking a pen and holding a clip-board --as with the previous scenario there is no life-or-death fight with the passengers.
He throws aside his silly name-tag and clip-board and immediately depressurizes the plane --the passengers are knocked out and later die. The transponders are turned off, they dive for the deck and turn to their destination four hours away --a 4,000 foot airstrip controlled by their fellow believers.
Immediately upon touching down the spoilers are activated, they apply maximum brake pressure and hit the thrust reversers on the pair of massive engines --the plane lurches, strains and jostles, but rolls to a halt at the very edge of their makeshift runway.
Dented technicals --pickups packed with angry-looking armed men-- stream onto the strip, guiding the behemoth aircraft packed with suffocated passengers to a rocky crag, with burly, bearded men camouflaging the aircraft even as the engines spool down.
Non-minaturized nukes are heavy, and a re-painted civvy a/c like the 777 will make a perfect delivery platform at 3,000 feet on a clear day at 10:00 am over a major city, the better to teach the non-believers with Allah's blinding white flash.
Scenario 3: Both pilots are terrorists. With assistance from grounds crew members who are in on the game they fuel up the jet with more fuel than normally scheduled for that particular flight. ...
Why not just buy a used commercial aircraft on the open market?
How about this theory. Plane takes off as it normally would. Plane gets to altitude and zap. All of a sudden radios go out. No one notices anything from the cabin. However in the cockpit, pilot and co-pilot realize something isn’t right.
They decide it is best to turn around. 15 minutes later there is another zap and the other radios go out as well as the black boxes. Also, every cell phone is zapped. The pilots, disoriented at 35,000 ft with a plane load of now panicked passengers start looking for land. Finally there is one more zap and the engines and hydraulics die.
The plane nose dives and heads for the ocean.
At the Whitehouse, a message is conveyed to both the Russians and Chinese. The message simply reads, “satellite test was successful.”