[niffiwan]

In this scenario you have a two part red alert mission.  Enemy big damned ship has red alert carry status, Alpha doesn't. 

I don't think this will work, as far as I remember the player wing and all "starting wings" (which defaults to Alpha/Beta/Gamma) always have red-alert carry no matter if the ship flag is set or not. You could maybe use variables (player or campaign persistent?) instead?

[headdie]

Somebody getting command of the biggest ship in the fleet, then in the middle of a border skirmish turning its guns on his allies and jumping away with the enemy. You could have a mission where your home-ship is escorting the shiny-new-toy on a shake-down cruise and get ambushed, only to have the ship turn traitor and blast your home-ship to oblivion and jump away.

This fails a basic fact: a commander going rogue while aboard a ship with several thousands crewmembers that aren't going rogue is a stupid commander, and soon a dead commander.

Mutiny involving a larger amount of crewmembers is a possibility, but again, aboard a ship housing thousands of crewmembers, the number of "loyalists" left is bound to prevent any kind of effortless mutiny. Not saying you can't do mutinies right, but you certainly can't have a ship with a large crew count go wholesale rogue. It just doesn't work.

Having the mutinees disrupt a capital ship long enough for the enemy to board it would be a good starting idea for making a mutiny right.

This brings up an interesting possibility of shifting "loyalties" of the ship as the two factions on board wrestle for control of the ship