In dialogue after escaping Peragus, Kreia discusses how she came upon the Exile while they were on the Harbinger, in this exposition she repeatedly says "we" as if she were with someone during/prior to the opening sequence though when we first see her she is alone feigning death, along with T3 and the unconscious Exile aboard the Ebon Hawk.
"You were difficult to find but coincidence was on our side. When I learned that you were on the vessel I knew the Sith would not be far behind. When we intercepted the Harbinger it was crippled drifting in space. It was a simple matter to board the ship and rescue you."
I've also been wondering, how did Kreia find the Ebon Hawk to begin with, I believe T3 explains that he had left the Unknown Regions in search of help for Revan and so he tracked you down but this doesn't explain how Kreia came into the picture.
Also, I believe in dialogue after your fight with Atris she reveals that she had arranged for the Exile to return to known space as a means of drawing out the Sith but what was the given reason to the Exile to explain why he/she was on board to Harbinger while it was on route to Telos to begin with, what could an Exiled Jedi have offered to the restoration efforts and is this even explained?
One last question relating to the opening, what was the "ghost" Sith Warship that first dispatched Sion and the Assassin's to the Harbinger and why had it been attacking the Ebon Hawk? Because by this point Exile is still on the Harbinger and if the ship had been returning from the Unknown Regions after 5 years there would be little reason for the Sith operating at that time to have knowledge of its importance.