I took a look at the book because honestly, I’m not sure! As I said, my group only played three sessions.
I think that mostly, what kinds of missions are available is dependent upon the location the legion’s in. Each location has certain types of missions, so selection may be limited. Each location also has a few special missions, which you can discover by spending Intel. They can also come up when the GM rolls a 6 when determining the number of missions available. The special missions also have a type (Assault, Recon, Supply, or Religious).
The Commander gets to say on what type of mission he’d like to focus. The GM rolls a d6 and uses this table:
1 Assault
2 Recon
3 Religious
4 Supply
5 Commander Focus
6 GM Choice
If the roll indicates a mission of a type not available at the current location, then you move up to the next number. So the Commander’s Focus increases the chances of the specific mission type he’d like. Especially since there are most likely 3 missions at a given location.
I didn’t recall all of this at all! There’s honestly a lot going on in this game. I’m reasonably sure I just offered the mission types available based on location, and let the Commander pick from those. But it’s a little more nuanced than that.
Ultimately, it’s dependent on location and the dice rolls, with the Commander having some input via Focus and possibly spending Intel for a Special Mission, and the GM having some say, as well.