I've replayed Sync, looked on few missions and found intresting things.
First are attacking fighters in first stage of champaing. Didn't anyone found strange there were always 3 Hercs
? Another strange thing is they arrive only in missions with Transcendant. Only in first mission first wing contained 4 Hercs. But most strangest is when Omega 4 destroys Alpha 4, it blows up along with it's victim. Also Alpha 1 can target only first fighter from enemy wings, but don't you think also Alpha 2 and 3 can target only enemy 2 or 3? It looks like attackers are some kind of mirrored "clones" of Alpha wingmen.
Second is that Pegasus fighter, which appears in M1 (nebula), M3 (inside jump node, it jumps out after few seconds of mission), M4 (inside subspace) and M8 (long distance from Alpha wing).
I've looked in FRED to all these missions, and found very intresting thing.
In first mission it's named "Unknown". In M3 "Darkness". But in M4 and M8 it's named "Penumbra". I've also looked at its waypoint in M4. It's named "PenumbraTerantoJump". Don't you think Penumbra Teranto could be real name of Transcendant? I'll redownload and replay Transcend and look at the name in FRED. Maybe i'll find more findings like this one.
Trird is about M6. There are 4 bombers destroying GTVA corvette, Archeon. When you try to destroy one of those bombers, you can't because they're invulerable, like Ransom didn't want them to be destroyed. Look at their codename. Beta. The same codename had bomber wing from Persistence. Maybe it sent them to destroy eventual witness and then changed their bombers to Ursas to don't make any suspicions among traders.
Fourth is about Beta 2. How did Beta 2 knew about Sync? Also, he "came through intense psychological trauma". I think i found reason. If you'll look at FRED to M8, you'll see Penumbra is jumping out along with everybody else. Maybe Beta wing met him in one of those systems. Then he somehow ordered Beta 2 to kill his squadmates and told about Sync. Also you should look at Beta 2's behavior in a mission, in which he gets killed by Shivan beam. "Did he lead us to that debri field for a reason?". It was written by Alpha 2 after that mission. I wonder if Penumbra tracked Persistence all along their way and gave orders to Beta 2 before his actions.
All events from Sync looks like planned. I bet Penumbra has got a plan he realizes during whole story. Maybe we'll find out what that plan is during later parts.
Still something bothers me. Who were those fighters player met in M7? Did they knew about Penumbra and wanted to stop him from realizing his plan?
EDIT: I've replayed Transcend, looked at some missions to FRED, and found evidance not only for theory about Transcendant=Phi 2, but also that some of Sync characters were "ported" to Transcendant (fanfares please
Look at that flash of Presistence group in E4M10 (mission, in which Sunder realizes, that Transcendant wants to be set free). First you can see Presistence and Farae jumping in, but then, there very short sub-flash, then it goes back to main flash. I've looked to that mission and saw thing, which explains everything.http://devimg.net/?Post=802
I think that's enough evidance. It would also look like Penumbra isn't Transcendant, but somebody else.
How have Sync characters found theirself in Transcend, we can only speculate (until Ransom will release another parts of Sync).