Don't do it! You know what you're thinking! Don't do it, don't-! ... You did it. You let your conscience kick in.

Shit! Shit, shit, shit! You can't rat them out! You actually like the Cutlasses! And if you throw them to the wolves now, you'll never sleep well again! Or at least as long as it takes for someone to collect the bounty Isabella would surely have put on you head. You let the despair of your own stupidity roll over you for one glorious, brief moment and then you snap into action mode. You turn to Rhian and grab her shoulders, shaking her slightly till her eyes are focused on you "Rhian, we've only got a little while to pull this off, so I need you to listen to me closely. Got it?"
She swallows and nods shakily "I'm listening. What do you need me to do?"
You focus your eyes on hers, holding her gaze "We can't fight them. Right now all we can do is let them get taken."
Rhian instantly swings at you wildly "NO! I'm not leaving my friends!"
You grab her by the wrists and grip them hard enough to draw a pained whimper from Rhian.
"Listen to me!" You growl "We can't help them if we're dead. But we can help them if we're alive and free. And in order to do that, you have to trust me."
Rhian's eyes are darting around like a wild animals'.
"First of all. I need you to remember this. On the wall to the right of the shuttle, you'll find a maintenance hatch. Get in there and follow it till you come to a section marked with seven green lights. Once you reach those lights, press all of them starting from right to left and then back again. All of them will turn blue and open up a smuggling hatch just above your head. Get in, close it and try not to make much noise. It's reinforced, cloaked and completely off the records. You'll have air, water and a few emergency ration packs. With me so far?"
She nods.
"Good. Next..." You wince "I want you to hit me as hard as you can."
"...What?"
"If we're going to have any chance of not getting killed, whoever that is needs to believe that you captured me and my ship. You need to punch me and stuff me into one of the lockers. And block it shut."
She's beginning to understand your plan. If you can convince whoever has attacked the ship that you're an innocent victim of the Cutlasses, you just might be able to talk your way out of this. Slowly she draws her fist back and you close your eyes "Try not to break the nose."
WHACK!
Your head spins to the side and you feel dizzy "Gonna need to be harder than that."
THUD!
Okay, that one actually hurt quite a bit "Needs a little mor-"
BANG!
Come on! Smacking your head backwards into the wall!? That's just low! You stagger upright again... just in time for a left hook to the eye. That's gonna leave a shiner. You wobble on your feet, trying to look through your teary eyes "Okay, get me into the locker" You moan as throbs of agony lance through your brain. To her credit, Rhian actually does try to get you into the locker gently. Unfortunately she forgot to check your fingers were completely inside the locker before closing the door.
CLANG!
"OW!!"
"Sorry!"
Well at least she sounds sincere. And if how you look right now doesn't get you some sympathy, it should at least help to convince anyone that you weren't in the locker by choice. You wait a few minutes (Hopefully long enough for Rhian to get most of the way to the hatch) and then start hollering for help.
"Somebody! Anybody! I'm in here! Please! I need some help!"
Distantly you hear footprints echoing as they move down into the main cargo hold, heading for the shuttle.
"If y'all can hear me, I'm in the shuttle! I got shoved in one of the lockers!"
Seconds later, you hear the door open and the locker door is pulled off its hinges. You'd be worried about that... if it wasn't for the fact that you now have a very large rifle pointed at your head.
"State your name and business."