I intend to follow a mission by mission stand point with us all participating in big story events which may or may not change the setting of our circumstances.

Sho will give you your missions as he's overall in charge of the whole operation how you receive them may be by courier, or by Jack in some cases. Small timeskips to skip travel time like any DnD game. Start mission, go through it, end it and find a way back to Kyushu hopefully without Britannian interference.