Space Adventure / War Short Story Identification

I read a short story in an anthology a couple of years ago. I can’t remember the name of either but remember the details below:

It was set on a gigantic colony / warship

The reader is slowly informed that there is a 1000 year war between an entire fleet of these ships occurring outside, i.e. a ship fires a volley of missiles and they won’t reach their target for hundreds of years.

The ship the protagonists are on has been hit and relatively disabled for so many years that most of the people on board no longer know they are on a spaceship and have fractured into several militant feudal societies.

The main plot follows a battle between some lower level kingdom and the pilot’s kingdom – each of which were genetically enhanced per their class, i.e. pilots were tall and could fly.

The main protagonist is some sort of captain or commander who is the last to remember his mission and has a talking bird on his shoulder – SPOILER – in the end he reaches the command room and fires a volley at a passing enemy ship/

This has been driving me crazy! Any help would be much appreciated 

EDIT

I’ve remembered a few random plot points…

• The bird on his shoulder was constantly saying something like “complete the mission at all costs”.
• There was a ‘marine’ who was genetically mutated to be massive and strong.
• The Pilot group was somewhat more aware of the situation and their leader at one point says something like “I was born under a blue sky”.
• The power on the ship has been off for many years because the captain made the decision to pretend the ship was incapacitated in order to fool the enemy ships nearby.