Space Adventure / War Short Story Identification

Question

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.

Answer 1

I recall reading this story (or, at least, a story very much like it) in the sci-fi anthology called Federations. It's called "Twilight of the Gods" and was written by John C. Wright.

The captain would be Acting Captain Weston II. Not sure about the bird, though the last Watchman does say "A true Captain would use the power, not for himself, but to complete the mission, and discharge the great Weapons the stories say our world carries at its Axis." As well, Valdemar, the former captain, carries a bird with him on each shoulder.

Regarding the pilots, "You dream of learning the Secret Word which controls that Ring, and of conquering the world, of driving back the tall elves from decks above, where they fly and know no weight,"

Regarding the marine, "The giant's shoulder was taller than a tall man's head, but his hair and beard were white with age. For he was the last of his kind, born to serve as a Marine, created by the lost arts of the Medical House, back when Twilight was young. His name was Carradock." As well, he says at one point "My father was an Earthman, born beneath blue skies."