Echo City by Tim Lebbon

Surrounded by a vast, toxic desert, the inhabitants of labyrinthine Echo City believe there is no other life in their world. Some like it that way, so when a stranger arrives he is anathema to powerful interest groups. But Peer Nadawa found the stranger and she is determined to keep him and the freedom he represents alive. A political exile herself, she calls on her ex-lover Gorham, now leader of their anti-establishment network. Then they recruit the Baker, whose macabre genetic experiments seem close to sorcery.

However, while factions prepare for war, an ancient peril is stirring. In the city's depths something deadly is rising, and it will soon reach the levels where men dwell.