I've had an hour or so of spare time in the evenings to keep working on this project recently, so I've been making progress! You've got to work while you have the chance, so I've been doing that. There have been some fairly major changes made, but hopefully they're for the better. The last version ends with tensions building with the Syndicate Extremists, and it will still continue from that point. I originally had that entire arc outlined and ready to go, but after scripting about 1/3 of the missions that were planned, I came up with an idea to flesh out that particular story some more. The ending also changed some, so there's that to work into the rest of the story. I'm now working on writing the basic outlines for the updated arc, and coding the new missions. It shouldn't change anything with the missions in the current version, so there should be no need to start a new pilot.
Everything is flowing fairly well right now, so hopefully I can get the new missions scripted fairly easily, and get a new update out at some point. No ETA right now, I'll just release it when it's ready.