P.S. Mothership here refers to all ships that can carry fighters and bombers; not just the Sirerian Mothership.
With that out of the way, what's up?
Fighters and bombers both need a mothership to reside in. If their motherships are destroyed, they'll do the following:
Combat/Patrol Situations
Rule #1 - Continue attacking their target first and upon its destruction, seek out a new mothership within the same sector only.
Rule #2 - If they're not engaging a target, it'll seek out a new mothership in the same sector only.
Rule #3 - If there're no suitable motherships, they'll wither and self-destruct gradually.
Deployment Situations
Rule #2 apply but only at the current sector. That means, if there's a ship with capacity in the current sector, it'll be auto-reassigned to that ship instead. Otherwise, rule #3 applies.
Operational limits
Fighters and Bombers generally operate only at the same sector as their mothership.
Fighters in fact, have a shorter range due to their commitment to safe-guarding their mothership MORE than attacking her targets. That will explain why fighters may suddenly U-turn when the target gets too far away (or is too far away to begin with)
More explicit behaviors can be defined for fighters, but I'll leave to another day, another big fat tip.
Have fun!