Drive

Humans has the pinch drive, courtesy of our rouge maker. Possibly also in the ship originally recovered by the emperor was:
1. The 'super gun,' also created by the rouge maker.
2. The 'maker' robot, possibly in the form of the ship itself.
3. Whatever's in the box.

I'm guessing this leads to 3 plot twists:
1. Some human figures out that how the gun works, which greatly aids in their battle against the continuum.
2. Some human discovers the 'maker' robot, which may also aid in the war against the continuum. The robot may be the ship itself, who's AI based off the 'maker' robot and is in need of repair.
3. Whatever is in the box...

It remains to be seen which of these spirits is causing the continuum so much distress. My guess is that it is the robot, currently in the form of the ship's AI, that they want back so badly. Maybe they don't care so much about the drive and the gun (although it seems that humans haven't figured out they have the gun yet). I suspect even the continuum don't know what's in the box.