Just went through Peragus again; and this was my conclussion:
HK-50 found you on the Harbinger; and crippled the ship to kill everybody and claim you his bounty. However the Sith Battleship with Sion/Assassins and the EH with Kreia/T3 caused trouble; and they kidnapped the Exile onboard. HK-50 follows.
End Harbinger... Enter Peragus.
Upon arrival HK-50 gets assigned at the maintance office. Coorta plans on trying to smuggle the Jedi out of the station; by locking all the miners in the dormatory and then contact some-one to smuggle the Exile away. However, as noticed, he never comes so far since HK-50 backstabs him for not agreeing with his ideas after helping in the begin to trap all the miners.
As for how HK-50 tries to escape... I would suspect he was awaiting one of the regular Telos-expresses to arive and hijack it. That also seems the only way how Atton came to Peragus; altough I have no idea WHY he should be there...