Piecing it all together *Major Spoilers* - Complete Plot
 

Alright so I played the (optional?) Alex mission right after exiting Beta Lethera 1.
Now Alex says that neither the corporations nor the empires attacked the transport.

Inoco (I didn't do the mission for them) said that triada attacked the transports and is holding the cargo.

I seem to recall it was the grey fighters lead by a rogue general that attacked the transports?

Yesy thats true. Do You have any problems with you game story line?

Well, if triada attacked the transport, then Alex was wrong right? Or am I missing something? Also I thought Alex was associated with the Grey fighters, or did I misunderstand that the first time I played through?

Alex wast wrong, he just assumed it was Triada as the evidence was created to prove him wrong. Depends on what game line You are Rouge Greys are guilty more or less as they were in kinda silence cooperation with Triada. You can find later that Rouge Grays capitan was just a toy in some Triada cooperative. Remeber that Triada wanted that Greys tech for themselfs, well better all new tech that is.