Earth has just escaped a period of occupation and the new order, the Coalition of Interim Governance, is hunting down all those it deems to have collaborated with the occupiers, the Qax. The Pharaohs--humans appointed by the Qax as governers, and given virtual immortality--are top of the list. But the Pharaohs don't see themselves as traitors to humanity; they see themselves as mitigators, ameliorating the worst effects of the occupation.
Negotiation with the Coalition, however, is not an option, so they run. Five generation starships set out from their base, Port Sol, each carrying one pharaoh and a couple of hundred colonists (for the Coalition isn't picky about who it makes examples of). Rusel is one of the colonists due to be left behind, but at the last minute a vacancy opens up. His scramble to reach the ship before it leaves is the first indication of the novella's coldness:
But there was a figure standing directly in front of him, helmet lamp bright, dressed in an electric-blue skinsuit, arms raised. As the car's sensors picked up the figure, its safety routines cut in, and he felt it hesitate. Nine minutes. He slammed his palm to the control panel, overriding the safeties.
He closed his eyes as the car hit the protester. (p.14)
Rusel is not a bad person--in fact, he is weighed down by guilt for his actions--but he is a desperate one. The power of the survival imperative is a theme that runs on through the novella.
This is a knowing story; humans have, we are told, been sending out generation starships for a long time now, and they think they know most of the potential pitfalls. They know the power of genetic and cultural drift, how possible it is for the generations to forget they are on a starship at all. So the ship's Pharaoh, Andres, institutes an iron order, a literal social contract designed to ensure stability over twenty millennia. Or, in her own words: "there will be no conceptual breakthrough on my watch!" (p.35)
To this end she uses some of her limited resources to establish a cadre of other immortals, in an attempt to provide continuity, memory. It doesn't matter, she reasons, if the transients forget; as long as they are stewarded by Elders then they can reach their destination safely and free. Rusel, of course, becomes one of the new immortals, eventually the only one, and it is through his eyes that we see the long march of years.
Baxter has a gift for capturing a sense of the deep future; he did it in Time, via a series of jumps through portals to the future, and he uses the same sort of episodic, logarithmic approach here. Throughout the book Rusel is constantly waking. He is woken by his brother to be told of the spare place on the Mayflower; he is woken after taking the immortality treatments, to attend to his new duties; and he wakes thereafter from longer and longer sleeps, to a Ship ever stranger and more dreamlike.
Things change over time, of course. The solutions that Andres so carefully puts in place break down (or looking at it another way, succeed too well), and too the journey of the ship is taking place over evolutionary time. Baxter suggests that in such an environment, where maintenance of the status quo is the most important thing, the selection pressure would be away from intelligence; and so, gradually, the transient population changes. The meaning behind their tasks vanishes. The cleaning and repairing become secondary sexual characteristics, like a peacocks' tail or the antlers of a stag: something by which individuals indicate their reproductive fitness to a mate. Innovation and curiosity are selected against. By the end of the story, the transients have become a perfect, instinctive starship crew.
As Adam Roberts notes in his introduction, life, for Baxter, simply is. 'Neither good nor bad, neither valuable nor valueless, just existing.' (p.xiii) That's perhaps as close as you can get to describing the central philosophy of Baxter's work; and 'Mayflower II' is perhaps as close as Baxter can get to dramatising it.