This is a funny story. Yes it's a bit long, but worth it I think
Big spoilers ahead, of course. Plus if you haven't done all the UC and Sysdef quests the story might not make sense
I made a new char and I was feeling saucy, so I used console commands to give me all the Starborn powers, just for fun.
I landed the Frontier at New Atlantis, doing the normal starting quest. When I got to the NAT, I decided to goof around and I cast Anti-Gravity Wave at the crowd. Everyone floated into the air, screaming, and it was hilarious. The guards didn't think so, however, and began attacking me.
This caused Vasco to go hostile to the guards, and a huge fight ensued. Vasco was remarkably effective, and after a bit I joined in, and we killed a bunch of guards. Probably some civvies died in the crossfire
Anyway, we survived, and I saw that I had racked up a 149,000 credit bounty. Haha! So we got on the NAT, and Vasco was acting like everything was normal. When we got to the Lodge, a guard nearby started attacking Vasco (but ignored me).
I watched them fight for a while, and eventually stepped in to help kill the guard.
Then we went into the Lodge, where I got greeted by Sarah in the usual way, and they gave me a room to stay in and everything. I guess they don't listen to the police radio.
Anyway, Sarah still wanted to take me to see her contact, that Tuala fellow. She became undismissable because of the quest, and so off the 2 of us went to MAST.
I tried to go into the building to talk to Tuala, but we got attacked by guards and other bystanders. Tuala ran out of the building into the streets, and I followed him, trying to get him to talk to us.
After all the nearby guards were dead, Tuala then started to give me his usual spiel about joining the Vanguard. This amused me, so I said yes. So what if I'm a wanted criminal, right?
He sent me downstairs to take the exam, but when I got down there everyone started attacking me. I ran around trying to find the exam, just to see if I could still manage to take it. Sarah was cowering in a corner somewhere. She was not pleased with me.
I could not get into the exam, but then suddenly one of the guards approached and instead of shooting me, told me I was being arrested. I surrendered, and got taken to the Vigilance to meet Ikande, who told me I was going undercover for Sysdef, and that I would be joining the Crimson Fleet.
I agreed to this, but as soon as they let me walk out of that room I attacked the guards in the docking area. I got a message "Sysdef is now your enemy!"
Sarah is still following me and complaining, and getting shot up.
Nonetheless, we managed to kill all the guards, get off the Vigilance and back into the Frontier, and also managed to grav-jump away before the Frontier got toasted.
I was free!
At this point I assumed I'd still be in big trouble if I went back to New Atlantis, so that's what I did.
Surprise, surprise, they let me land, no problems. Sarah (who was mightily ticked) still came with me to talk to Tuala again, and now he was friendly. Everyone was friendly.
It seems that when I accepted Ikande's undercover offer, Sysdef paid off my bounty. I was clean again. Even though I shot my way off the Vigilance, I did not incur any further bounties doing that, apparently.
So, I'm clean, no bounties, after going on a killing spree in New Atlantis, which is funny as heck to me.
I'm sure Sysdef still hates me, but the UC is happy with me and still wants me to join. Sarah hates me but can't leave because she's undismissable at the moment.
That was almost too much fun. Now I plan to go elsewhere and see what other trouble I can cause
TLDR; I racked up a huge bounty in New Atlantis as soon as I first arrived there, got arrested and taken to the Vigilance, accepted the undercover offer, but then fought my way off the Vigilance and escaped. I wound up with no bounty, and only Sarah is mad at me.