Okay, i played Transcend, and it scared the snot out of me, but i still dont get it. Is this 'transcendant' in the pegasus, did he supposedly fly to the EDGE of the universe and come back with some sort of special freaky powers? or is it just some nebula ghost?
Transcend's story is possibly one of the most confusing and open-ended storylines I've ever come across for movies, campaigns, books, et al. That's not a bad thing, as speculation is good, but I don't think anyone's come across one definitive theory yet.
If you listen to the Transcendant's messages and then play Sync, you'll notice some startingly similarities. Not just coincidences like "Yes, sir" or "I'm going in", but really key lines from Sync are present in the messages. For example:
"Me to--luck, but I'd rather take my cha--...ivans" (Transcend--dashes and dots are distortions)
"Me too. Good luck, but I'd rather take my chances with the Shivans." (Sync, one of Phi wing's messages before leaving the Persistence)
"It isn't our time to die!" (one of the Transcendant's final messages)
"No, damn it! It isn't our time to die!" (Alpha 3's line when encountering the Hedetet)
That leads me to believe that they're some sort of Sync-Transcend connection other than just being a side story, as if the Transcendant was one of the Sync characters, or an onlooker in Sync. Compare the Transcendant's Pegasus with the unknown Terran ship in Sync's first mission for real confusion.
There's also some other references in Transcend. If you're a fan of sci-fi horror, some Transcendant lines should be familiar: "Do you see?" followed by a short, sharp "No!" were the last words of Sam Neil's character in Event Horizon. When you compare Event Horizon's story to Sync's, you see similarities: a ship is sent to the far reaches of space through the use of a powerful subspace drive, and then returns several years later and brings all sorts of nasty with it.
So, basically, my theory is that one of the Sync characters, most likely Beta 2, since he was closest to being the one who wanted to stop the Sync drive before it destroyed all of mankind. When he was killed in the last few missions, he must have transcended beyond his reality, and used his new power to lure Marcell and the Shadow Hunters to him to kill him. Now, you might ask, what good would killing Beta 2 do if he had already been killed? Easy--that purple nebula where all the weird crap happened must've been where the Transcendant was fully able to alter time, and if you killed the Transcendant (i.e. Beta 2) at the right point in time, Beta 2 wouldn't have existed. Therefore, the Persistence wouldn't have had an escort, and therefore the events of Sync would likely have not played out.
You can see the Transcendant trying to alter the events of Sync in the early parts of Sync itself through eliminating certain characters or stopping the events. First, he tries to collapse the node in the first mission to keep Alpha wing from ever making it to the Sync storyline in the first place. Second, he sends out those mysterious waves of Hercs throughout the first few missions of Sync to try to kill off Alpha wing and the freighters before they reach the Persistence. Finally, he attempts to totally stop the Sync events by sending in the Carthage to arrest all of the main characters, and that's when Persistence panics and uses the subspace drive. Beta 2 going mad after the jump may have been the Transcendant (i.e. his future self) possessing him (you don't see the Pegasus at any other point in Sync, plus Beta 2 tries to destroy the Farae in one mission and consistently warns the Persistence crew about the Sync drive).
Now, the final subspace mission in Transcend. There are two possibilities as to exactly what this is. One, it could be, as I theorized earlier, that the Transcendant (Beta 2) was using his powers to go back in time slightly to make it possible for Marcell to kill his past self (before he was an escort for Persistence in Sync), and therefore the chaos theory might lead to Sync having never played out at all. Another theory is that that node that you enter might be the same node that the Transcendant tried to collapse in the first Sync mission. By bringing the Chondral, Generation, et al. into the corridor, he set about the process of finally collapsing the node, and killing the Transcendant may have brought the being some closure or a release from his state (his last words are "Thank you" just before he sends Marcell back to his point where he had started intervening). Killing off the Transcendant, the Shadow Hunters, and all of the main characters other than Marcell and the guy you escort in the first Transcend mission sets everything back to normal.
In the end, you have Beta 2 dead, so Persistence is without an escort, and the node that Alpha wing wanted so badly to escape through in the first Sync mission collapsed, leaving Alpha wing and the Tether either lost or dead. Therefore, the events of Sync never play out. Once Marcell's part in Transcend is over, he's sent back to his own time.