I have a question on side missions. I know that after playing "Aftermath," the heroes draw two side mission cards from the previously assembled side mission deck and choose one to attempt.

But in subsequent side mission opportunities, does the one they didn't choose stay on the board as one of their two choices? Like, they get one they really don't care about, would it just stay out there all campaign as the heroes keep picking the other option to play? Or do you shuffle the unselected mission back in to the side mission deck and draw two new ones?

I'm pretty sure it's the first one from my read of the rules, but I just wanted to see if anyone else had taken a closer look at that than I have. If it's the first, I expect "Viper's Den" will spend the rest of my campaign sitting out there unwanted.

yes the mission they don't choose stays there

Viper's Den is the one with the Rebel Recon reward, right? Take it as early as you can, that card wins games.

So they draw two, pick one, the other stays until picked. What if I play an agenda card? Will the one that stayed and the agenda result in drawing no cards next side mission?

I believe that the Agenda mission would have to be played after the second mission had been dealt, so the Rebels would have their choice of three at that point.

Obviously whichever they choose, the Agenda mission won't be active once they play the next mission.