Need to start thinking of a setting or story name so I don’t keep calling it the lame “space smuggler story”. 
Possible change is: the lead character is contacted by his sister who he is estranged with (details of which come out through the story). She’s in danger and needs his help. Recklessly he gets his band of smugglers past high security gate points to a empty star system far off the beaten path and finds an empty prototype starship. Aboard they find signs of a struggle and finally find his sister, possibly alive with a few others. They have a powerful new reactor that the government wants as a weapon, but they don’t want it used as such and barely escaped. There is a peaceful, neutral science-oriented culture who lives on a planet within the realm of an enemy interstellar nation, and they want to deliver the device to them to give them abundant power and let them continue to study the new technology. The enemy nation won’t benefit (and upset the balance of the ongoing war) as this planet nation is a space-age Switzerland, it only resides within the space of this nation (and is thus protected by the armies of the other interstellar nation that wants to use this device as a bomb).
The truth is though, the original message was from his sister who was on the ship. The army decrypted the message and took the ship. They placed a biomech on board (1 or more). They are androids whose organic external layers can morph to take any person’s shape. The biomech killed his sister, tore her memories from her implants, and is using the main character to smuggle the device past enemy lines (where it can be blown up near a moon in the same star system as the science planet, which is a major naval base for the enemy star fleet).
At first tricked, as the trip progresses and the hero makes amends with the devils of his past (something about abandoning his sister and his family or doing something they didn’t approve), he discovers the truth and fights it out with the biomechs. In the end he is victorious, but it is a bit of a hollow victory as he mourns his sister’s death. He regrets he could not make amends with her in person, but he is glad that he has healed that wound in his soul at least for himself so that he can move on past it.