Another idea just occurred to me. I was thinking about the similarities between the ships in Sync and Transcend, and I think I have an idea on what exactly the Transcendant was up to.
In Sync, the fleet carrying it (the drive) contained one Deimos, one cruiser, one freighter, one transport, and several fighters.
In Transcend, the fleet in the tunnel contained one Deimos, one cruiser (the Silent Eye), one transport (Sinclair), one freighter (Chondral), and several fighters.
It seems to me as though the Transcendant was trying to reconstruct the Sync drive by reconstructing the fleet that carried it. The only pieces missing were several more fighters, hence why he was after Omicron wing. In this context, his plead of "help me.... help me.... HELP ME..... PLEASE!" makes a little more sense, because he wasn't asking to be killed, but rather asking Sunder's help in reconstructing the fleet.
If the Sync drive was the reason he transcended, maybe he was trying to reverse the process.
Just a thought.