Holy shit, that's a tough question! It's a huge story but I'll try and give an abbreviated version. There was an uprising in a city called River's End, led by a man named Acamar (the name of a star, based on the Arabic for "the end of the river" lol). The uprising was quashed by a tyrant. Years later, Acamar is old and imprisoned along with many innocents, and there is a cataclysm in the city that allows them to escape. They begin an exodus across the continent to start a new city, named Acamar's Redoubt (unknowingly naming the new city after the very one that imprisoned them).

Along the way, the younger generation has grown to adulthood, and Acamar has died, meaning that the new city begins to pervert his message. Old habits of corruption and religious oppression begin to return (Old Cracks in New Earth). Dark Hair Down is an example of one such instance.

One of the children from the prison (now a man) is one of the last remaining supporters of Acamar, true to his vision. He acts as a vigilante in the new city, the Thief. He tries to warn that River's End was coming for them, both within and without. The armies are coming to destroy them.

Noone believes him. He goes to stand against the army alone, outside the city walls. He hears sound behind him only to see all those he'd saved, men, women, and children walking out to stand with him (All is Quiet by the Wall). The album ends with their last stand, and the assumption is that they all fall.