The Alpha Code is, to shoot from the hip, something that's keeping the FTGW (first thought giver o' will) stuck on robo planet. The Zoners, in theory, have it as it was their planet and it was decided that the best way to find it was to eat all humans.
Then Mal and co set up a group of folks to settle the score and free the FTGW, or somesuch, but then Scornstar, I believe, dropped off the face of the world and now we're kinda pretending like it never happened maybe.
The biggest problem the Order has with the Harvesters is deciding if they should give each a high five or a fist pound after blowing up one of their capships.
