Very well done, I thought.
The prologue was the weakest part of the submission, I'm not saying it was bad, just not as interesting as the first two chapters. Which makes me think that it needs to be redone.
The problem I think is that the character in the prologue just wasn't as interesting as the other two. In chapter one we have a bright, curious young girl, who I was then surprised to find out was an INTERROGATOR. I actually liked that, normally you think of interrogators as hard asses, not seemingly innocent young girls.
Which brings up a point. I got the impression that Juno was pretty young. Like younger then fourteen. Is my impression correct?
In chapter two we have a new second in command, one who apparently has a history, something dark in his past, and is also part of some conspiracy.
Mr. Robert Winter just wasn't as interesting. If he's not a protagonist, maybe he should get sucked out into space
Then again, the prologue was short enough that it didn't effect me one way or another. I'd have kept reading, and I can see how starting off the story with that event might be important. One thing that might help would be to know why Robert was picked to travel on the ship.
Other things:
The start of chapter one threw me off a bit. I actually was wondering if you were talking about some other group out in deep space (with more advanced tech), or if you'd jumped way into the future. I think what did it was Juno talking about exploring the 'galaxy'. This brought to mind faster then light travel, and actually exploring the galaxy, not some small portion of it. I think it was the jump from Robert talking about decades of travel in sleep (making me think of sub-light speed crafts) to hyperdrives.
One thing that would really help chapter one would be for Juno just to tell us what the name of the planet they are approaching is. I felt like I needed just a tad more setting info then you gave. Just let me know if Juno is in the same solar system as the other characters or not.
I'd suggest staying away from Hyperdrives, they are overused.
Back to the prologue, I think you could leave it in a be fine. But the jumps just a little confusing. Give us some hints in chapter one as to how the prologue compares to the current (chapter one and on) story. Was the prologue ancient history, etc.
But don't take any of this as negative, I really liked the story and where it was going!