Earth is overpopulated and lots of those people belong to groups who don't want to exist with other groups, so colonies set out to take planets. After some time, all the planets but one have almost died out because they used Earth-like planting, building, etc. instead of finding out what that planet needs. There's a spaceship & city group called the Authority and they move between the planets and take messages. There's shipper groups, too. At the beginning of the Diversity Crisis, the Authority sent a ship back to Earth for help, but even with quarantine and sterilization, many Earthers die. The colonists, named the Called, and everybody else in space, is barred from Earth eternally.
The one planet where the people are still alive is Pandora. The "family" run their complex domes and manage villagers outside the dome. In the dome, everything is good. Outside, almost everything is like an outside jail. The hothousers (village slang for dome people) will come and take people to experiment on their organs for just about any infraction, and sometimes just because they want to. The hothousers have a "Conscience" in their mind, and each dome has an AI that runs the complex. Our complex is Aleph.
Athena Station is managed by former Pandorans and also has the commander of the Authority and her crew. There are too many people on the station and Helice Trust takes her tween girls down to the planet to get a job she was promised. Chena establishes a messenger business to the next town while her younger sister, Teal, not only does her required work, but Chena's as well. The money is split between all three of them. They meet Nan Elle, who is the "poisoner" in the area. Real medications aren't allowed outside the domes, so Elle and the other Pharmakeus illegally make medication from the planet. Chena frequently runs her secret medication to the other town, too.
The Authority has threatened Pandora with destroying them if they don't find a cure for all the Called. To enforce their threat, they bomb a desert and promise to bomb more. This makes the family -- hierarchically linked people -- very worried and they start to experiment more. They particularly want Helice Trust because they think she has the closest immune system to carry the healing fetus without having it die. Helice doesn't want to go, but she loses her job and is otherwise manipulated by the hothousers, so she and the girls go into Aleph.
Chena is very unhappy there and shows it. Teal is very unhappy and plays along, thus getting more access to things. One day, though, they hear a scream and rush to their mother's alcove. She's dead and there's blood everywhere. The baby is gone.
We find out that a member, Dionte, of the lead family in Aleph has taken the "Eden Project" to kill the Called rather than to help them. She has not only changed her Conscience so she can make others agree with her, but has changed Aleph in the same way. As the book progresses, Aleph begins to know something is wrong, but Dionte has "fixed" the tenders' Consciences to not believe her.
Five years later, Chena ia an apprentice poisoner and Teal has run away to go back to Athena Station and find out what happened to their father (the others have always believed he ran). When she gets there, the station has people left and right and is more like a prison than a home. She does find that her father ran and that he is dead. The hothousers make a deal with the station chief to send Teal down, so they can use her for her eggs and immune system, but when she gets there, she's greeted by Dionte's blood and family brother, Tam, who had been helping Elle and them. Dionte has changed him, but he's not quite done.
Chena has made it into Aleph to take "poison" to a client, who turns out to be Dionte. She is shut up with Basante, Dionte's assistant, and the man who killed her mother and stole the Eden Project. She uses some of the real poison that's hidden under a false fingernail to poison him. However, because Dionte knows how to make rooms so Aleph can't see them, Aleph doesn't know Basante is dying until Chena tells her and Chena bargains to get out by telling Aleph where Basante is. She gets out without telling and Basante dies.
Teal, Tam, and Elle know where to find the Eden Project, but Chena is ahead of them. His caretakers have caught her, but she gets him to let her out. She talks him into getting out with her, but on the way she kills Dionte, and two caretakers. She hits him to keep him from running away and takes him out on the cliff, planning to jump. Aleph has kept track of all of this and shares it with the other AIs. They know things have to change.
Teal gets Chena to give her the Eden Project and they head toward a safe place. The family is told that all the Called and shippers will be moving to Pandora and the family says no. However, Aleph says yes. She explains how the Consciences have been screwed up and how she and some of the other AIs were changed without their knowledge. They're going to take out the Consciences and welcome the refugees and make it work.
I thought this was kind of slow at the beginning, but then it picked up. There's a lot of teaching in the book; I hope she doesn't start writing like Sheri Tepper.