I've just seen the episode The Dwarf Star Conspiracy and the Big Bad has finally revealed their presence directly.
When Rook is reporting to his "boss", he says he is only 24 years old, but is dying of old age.
And if a solution isn't found, Rook "might be next".
I had assumed that meant that his boss would be transplanting his brain into Rook's body, but given the recent events, I have a new theory.
That his boss is one of the invading aliens in a human body and the effects of prolonged inhabitation are causing the body to wear out.
This is confirmed in the episode, that only a body with the self-repairing nanites can be a successful host, because they constantly repair the damage done by the aliens.
When Suki starts timeshifting, she eventually meets Future Five, who mentions that "so much has happened" and one of the events listed is something called the "black ships" and that the Rasa has been taken far out of known space to hide, probably to avoid them.
In this episode, it is mentioned that having an army of superior soldiers means nothing if they don't have ships as well.
I am wondering if the black ships are the vessels owned by the invasion force and they were constructing their armada somewhere else in preparation for conquest.
The name was probably given to them for identification purposes, since the invaders haven't named themselves and in their natural forms, they are black.