So here's the deal:
A few weeks ago IRL, Daria and Zepar unlocked a room in the spaceport with the Omega Key, that served as a control room for Salvation's docking cradle. That's why she was suddenly disassembled, which caused that prison riot earlier- the activation of the room triggered a repair protocol.
Zepar has found a device in that room that can scan objects and use them to create upgrades for Salvation. So far, he's improved her interior defenses somewhat and given her shields and regenerative hull plating.
Y'all collected a lot of stuff back in Part I; this is a way you can put it to use.