Relatively easy to incapacitate over 200 passengers??? How exactly? The only hijacking scenario i can think of is if one of the pilots does it by taking out the other with no one knowing. They’re flying in the middle of the night, and none of the passengers really know anything is wrong.
I assume there is access to the ventilation system through avionics. You don’t think the pilots could smuggle gas masks and knockout gas grenades on board? That is what I’d do if I was trying to hijack it.
You gradually decrease cabin pressure until they’re all asleep, then dead. Easily done in an hour.
Serve them all the fish for dinner.
Put on a gas mask and gas the whole lot of them, while most are already asleep. Proceed with whatever it was they intended to do. Turn off transponders, fly at low level back to PETRONAS towers, etc.
Perhaps the mask fails for some reason, the pilots are incapacitated, and the plane then flies on autopilot until it runs out of fuel.