Ok, to set a few things straight.
The Sith where on a "Sith Warship" as they are always talking about on the Harbinger holologs. They where talking about how there was a battle between the Ebon Hawk and this Sith Warship and the Harbinger went off course to go and investigate (Keeping in mind that the Exile was on the Harbinger, and their set course was Telos, Exile being a member of the Republic - Soldier or whatnot, I believe)
Ok so the Harbinger investigates this, and they find the Ebon Hawk which is damaged from battle and they dock it with the Harbinger, and I think that they found Kreia (which I dont know how she got there, but I dont think it was from the Warship) And T3. T3 was probabally searching around for whoever Revan wanted him to go and get (Exile probabally)
A team of Republic soldiers were sent to investigate the Sith Warship but then found that it was Empty, the Sith Assasins onboard it then boarded the Harbinger, keeping quiet still. Sion who was with them was found as a corpse I believe and taken to medical section of the ship. Now the Sith assasins where waiting away, on the Harbinger and when Sion awoke and asked "Where is the Exile..." or whatever, he and the Assasins started to wreak havok killing and destroying anything to get to the Exile.
Now the whole Republic crew was killed, and the HK unit on the Harbinger was programmed to protect the Captain, but because he died, and so did everyone else he protected the Exile and dragged his unconcious body into the Ebon Hawk, as to which the escaped to Peragus.
Hopefully I didnt spoil too much.