All On Syphon Filter

get killed?

On SF Central this question goes on for a few pages now. This never even crossed my mind as I always throught that the pilot was killed because he screwed up and made Logan escape. But this would also mean that Chance was expendable.

Watching the scene again makes it obvious the first shot targeted the wing and seems they were waiting for everyone or at least Chance to get out. So maybe they killed the pilot for being overzealous since the Agency needed the Data Discs which isn't guarenteed that they survive.

Maybe Chance did radio Archer or Morgan that the Data Discs were kept in a fire/explosion proof box. If that's the case I doubt Morgan or Stevens wouldn't hesitate to kill Logan and don't care about Chance. But who knew how Logan could evade a whole unit of "trained" commando's, jump clear of a missile twice, get past a tank, a C4 Wired bridge and jump on a train like that, I still wonder how he could do that. And then evading an organized squad like that and getting the Data Discs from Archer was pure luck.

The Agency never expected Logan to get off the mountain alive or without getting captured. Still then I wonder why that pilot get killed. He did his job..

I don't know if Chance was expendable on the plane. Obviously the plan for the attack pilots were to make the transport crash and not burst into the air, because the Agency wanted the disks.
Archer says on the bridge that everyone is expendable. Although this probably doesn't refer to the whole operation, beginning on the plane, it may outline the line of thoughts of the Agency leaders. Chance probably was one of the most valuable agents of the Agency, yet they probably would have accepted to loose him if it were to insure Logan's death and gathering of the disks.
Now, as to why the pilot gets killed by Morgan, again it's hard to answer. Yet it wouldn't be the first time in movie/video game history that a bad guy kills one of his subordinates even if he had nothing to do with the failure of the objective. Morgan seems to be the kind of impulsive man to do something like that. Obviously he expected from that opration that no GIs survived, and Logan above all. How could the pilot have ensured that, yet making sure the disks didn't get destroyed? I don't have a clue.