At this point you can unload any loaded ships from their carriers.  An unloaded ship winds up in the same sector as its carrier.  If the cargo and carrier ships belong to different empires, then either party may unilaterally unload the cargo.
 
If you have issued a fire order for a loaded missile or deploy order for a loaded device, it will automatically be unloaded during this phase in preparation for use.
 
Abandoned Empires: Any loaded conquering ships will be unloaded at friendly or allied worlds, or at worlds where they will be used in combat (see below).  Loaded missiles will be unloaded if they are to be used in combat at foreign worlds; otherwise, they will remain loaded.