The plot is that a man called Egil has taken knowledge from the Akashic Record (which contains everything in its writings). Using this knowledge, a specific incantation, he takes control of the Throne, using it to destroy the world he thinks will only continue to suffer if it is not destroyed. He has lived for 600 years, and he has seen the horrors of war, famine, blah blah blah . . .
But the main character- the "hero"- Raleigh Lovelace, he grew up in a Children's League Facility, which is basically a fenced-in ghetto for orphans with policemen in charge of them. He escapes with Becca Cardona, and they're briefly taken in by some bandits. There they meet a young girl named Mia who shows them how to get to the Capitol City of Anacrusis- by riding on a giant bird called a sky whale.
The sky whale is shot down, (there are guns, by the way, but only in upper-class and police/milita hands) and when the police try to apprehend Raleigh, he kills three of them, escaping. They arrest Becca (sky whales are considered dangerous monsters) and throw her in jail.
Raleigh meets a boy named Clon who helps him bust Becca out of jail, and they all hide out in the basement of Leonne's magic shop. Leonne is a skilled mage who teaches them how to do all sorts of enchantments and dark magics, but eventually the government catches up with him, and he's moved out of Anacrusis.
Leonne, with the three kids in tow, rides a train to the prison town of Penitence, but it derails and runs into the base of a canyon. Raleigh uses magic to throw as many people as he can out of the train in time, saving a dozen people or so.
The cause of the derailing was an explosive set by the Dragoons (thieves from before), and they intend to kill all the survivors, but Mia convinces them to just steal all their belongings. She has a good laugh and tells them they aren't far from Penitence, and if they keep walking, they'll reach it quickly.
In short, they do.
Raleigh finds out about a magical technicians' program going on in Penitence, and he applies. He's made second to the head of the classified project, known as the Completion Initiative; its goal is to make humans immortal.
Leonne opens a new shop in Penitence, and Clon and Becca essentially become errand-runners for a while.
As they CI draws to a close, Raleigh messes with one of the spells, his justification that no one should be allowed to be immortal.
When the project ends and the "God Machine" is finalized, lottery is drawn with each of the 400 workers' names in it. By sheer force of irony, Raleigh is selected to enter it first. Enter a machine he has altered to kill instead of immortalize.
It does kill him, but he manages to correct the error in the middle of the process, and the machine revives him.
The God Machine dies in the process, leaving Raleigh as the only immortal. When Emperor Gothos gets wind of this, (the project was mostly for him) he orders Raleigh to be an outlaw of the highest caliber.
He runs around for two years, jumping from town to town, but eventually returning to Penitence to meet his old friends. Once reunited, they decide to form an anti-government faction: the Outcaste.
The narration begins about four months after Outcaste's inception.
tl;dr: Raleigh's life sucks. He becomes immortal on accident. He runs away from the law for a while. He forms a rebellion.