I'm assuming most of the main story is based on the "Head to Meteor Falls" and "Stop Team Sky" in the active tasks. However since they don't track, it seems like you can kind of get lost and unsure where to go to progress further in the story. For example, when you have to back track to a few...
I was stuck at this part for a bit too. Managed to somehow figure it out after a couple of hours running around.
Have to go back to Fortree city and talk to the npc standing outside of the bottom right hut in the city. I'm assuming this is the part you needed to progress.