Actually I am still reading the Mindjammer rules, they are pretty thick and I am about half way through. The Fate system is interesting. I like the fact that you can use Aspects in such interesting ways, to make a gaming system quite player friendly. They can also be used by a GM to make your life a little miserable, but to enhance the campaign.
I have done some preliminary brainstorming on the Star Trek, but I haven't solidified my thoughts yet. I have figured out some of the crew, and as I mentioned the ship is using a brand new type of Warp Engine, the Hyper-Warp drive engine. It lets you travel at x10 normal Warp 10 for every level of HyperWarp -- HyperWarp 2 is x20 normal Warp 10. But the way it works is that you open a portal into HyperWarp space, travel a certain distance and then open a new portal and exit into normal space. But... there are strange things about HyperWarp space, some very disturbing rumours of experimental flights from the Klingon Empire and the Romulan Empire, who also have Hyper technology.
The USS Hermes is the first ship in Starfleet capable of regular HyperWarp travel, although you can "only" go to HyperWarp 3, which is x40 times faster than Warp 10, which means you going really really really fast!
Travelling on short trips, making HyperWarp jumps, seems safe, although travellers always get a "bad" feeling, like someone or something is watching them, something terrible is going to happen/has happened. Basically a "creepy" feeling. And as I mentioned there are rumours from the Klingon and Romulan empire about something happening in HyperWarp. The Kingons, despite being allies, have not shared any information, and the Romulans are of course not going to share.
Your primary mission would be to explore this new region and report back to Starfleet. The game would take place after TNG, after the movie Nemesis, and the Dominion war. I am not sure how much later but somewhere around 20 or 30 years.
There are sentient androids who are built using a system that was designed by B4, the Data like android from Nemesis. Actually B4 has Data's memories and used them to grow as a person would, to evolve. He now calls himself Forward, and runs a -- not sure yet about the particulars, but a group of Androids.
Since Forward evolved from Data's memories, he has only been able to create Androids based on someone else's memories, which fits into the Mindjammer game quite well. Also the Androids can interface with a Starfleet ship, and act as the Ship's avatar.
I am not sure if the captain should a player or an NPC, or I was thinking about making him a Hybrid character. The Captain would be played by one of the other PC's, in addition to their normal characters, and the GM would take over at times. During routine missions, especially outside HyperWarp space, the PC could play the Captain. During certain missions, and at times in HyperWarp, the GM would take over. There are a few reasons for this, but one of the main reasons is that the Captain is not supposed to go on Away missions, at least not until the Away mission checks out whatever they find and report back. Also, the Captain may know more about HyperWarp than he has shared, maybe due to Starfleet Intelligence or something else.
We would probably start with a few missions where your characters would get to know each other, probably in Starfleet space, but they might also be in HyperSpace. Once the character's know each other and are comfortable with the setting, we would jump into the main HyperSpace campaign pieces. The first missions would be a combination of Starfleet sending you somewhere and probably the team just exploring space, like Star Trek TNG did at times.
Well that is some of the campaign I have come with so far, there are more ideas I need to solidify. A lot of the campaign would also come from your characters using their Aspects, and how they explore HyperSpace, which as I mentioned does not seem like quite a safe trip.