Rogue Stardance by M. Garnet

Take an orphan girl and raise her on a space freighter that has hidden assets and an unusual crew. Let her grow up to become the owner and the Captain and know the way of the space lanes better than even the Federated Ships.
Give her a good life, and then one day, she makes a mistake by doing the right thing out in the deep dark. She answers the call for help from a small stranded ship and discovers what every scientist has been protecting for centuries––aliens.
But as an orphan, she had been brought up as a family on this ship, and she would help the tall stranger in the black liquid armor, and his warriors find a way home.