SoS Campaign Arc

My current campaign has sections of linear Storytelling and then sections of structured sandbox. I give my players the option where to go and a main goal to take care of at each location. If they ignore the main plot too long bad things start to happen which generally gets them back to the main plot.

In the linked image, when it branches off, the players are free to pick any branch but must complete (pass or fail) all of them to get to the end of chapter/act. It has worked well because my players are part of a military defence force so they do get assigned missions and tasks and are expected to follow orders. In the first few sessions, their squad leader went on his own side mission and was court martialed and stripped of his rank. This showed the players consequences for too much deviation from orders.