Basically to me this song is the end of the story. The crew has become exceedingly notorious for the spacetime bending powers they've harnessed from The Chronomancer. They've probably committed all kinds of crimes and had cults centered around them etc and now the shit has finally hit the fan. Two huge intergalactic space powers have seized an opportunity to catch them and have assembled their space fleets right where The Sword is, and they're all going to blow the shit out of it. However, the second Chronomancer "kept her promise" and tears a hole in the universe through which The Sword can escape, hence the lines about "nothing can remain the same" and "This is the hour of the Phoenix when all must be reborn in flame" because now they're starting over in a whole new universe and they can never go back to the old one after fucking around for who knows how many thousands of years.
Basically to me this song is the end of the story. The crew has become exceedingly notorious for the spacetime bending powers they've harnessed from The Chronomancer. They've probably committed all kinds of crimes and had cults centered around them etc and now the shit has finally hit the fan. Two huge intergalactic space powers have seized an opportunity to catch them and have assembled their space fleets right where The Sword is, and they're all going to blow the shit out of it. However, the second Chronomancer "kept her promise" and tears a hole in the universe through which The Sword can escape, hence the lines about "nothing can remain the same" and "This is the hour of the Phoenix when all must be reborn in flame" because now they're starting over in a whole new universe and they can never go back to the old one after fucking around for who knows how many thousands of years.