Its probelly allready put out there, but a expedition that gives a living frieghter as reward, maybe?
Or a long quest line wher u get a message from unknown source that leads you to a damaged living frieghter (like a mother for the living ships) and u have todo a series of missions to fix the living frieghter, and at the end u can chose to swap the living frieghter with the current one or let it free... But if u set it free theres allways a big change she will be attacked again, so safer to swap out with current frieghter (little story line)
I have plenty of ideas but this one seem somewhat for this game