I wonder why I remember another story where there was someone becoming either the ship's controller or something and participating in virtual battles for cyber warfare...
The virtual battles being done so that it's armies besieging castles. One battle had phalanx, another had a million "peasants" that took in "code" that was defeated and upgraded itself with it...
P.S. I didn't check up on it for so long... It's been taken down from Syosetu... Wow...