User blog comment:Solowing106/WMD Catalyst fail in AC6/@comment-1824272-20120831035439/@comment-1824272-20120831233746

There was an spy on board who shot the captain, killing him, and the co-pilot, injuring him. Most likely, the other staff or crew on board took the gun from the spy and either restrained or killed him.

I always thought that he was Yuktobanian, because the Yuktobanian military did know about the covert op (the Yuke PM should have, cuz he was headed to North Point as well, but we know he didn't have the same intentions as his military). Then again, just how did Yuktobania find out about the covert op? It's been sort of decided that the 8492nd must have leaked them this information (as well as how to penetrate this far inland, similarly to missions 11A/11B and 17). So maybe they wanted Yuktobania to be the ones to assassinate the President, either in the plane itself or by air attacks; however they did it, at least the President's death would just ignite the fire of hatred in Oseans even more. But when the Wardog Squadron came in and went all "Get yo asses out of here, Yukes," they deployed their main fighters to intercept.

I suppose this is one of those things where we can just keep assuming all we want, but we'll never come to a conclusion.