My players just won Aftermath. The book says put a new threat into play. Do they do that immediately? The campaign log has a spot for a side mission before story mission 1. Just want to make sure I do it correctly

It becomes the active story mission, which means it will be played when the campaign log tells to play the next story mission.

After Aftermath you draw two side missions from the side mission deck. Those become active side missions.

You check the campaing log and see that you should play a side mission next. So, the rebels choose a side mission to play from among the active side missions.

When you have played the side mission, draw a replacement from the side mission deck. There will always be at least two side missions to choose from.

Are the side missions drawn randomly?

Nvermind. I found the rules. I just missed them on my first read.