The Reckoning. The Bone Gardeners Trilogy, #2

The tunnel network is dying. Three weeks after stopping a life-extension ritual that would have enslaved her city, Kira Blackthorne discovers the corruption runs deeper than anyone imagined - a continental conspiracy to replace natural death with artificial immortality for the elite. Hunted by converted bone gardeners whose minds have been rewritten to serve the immortal council, Kira must master ancient Counter-Codices that her ancestor designed for exactly this crisis.
But accessing knowledge powerful enough to reverse magical corruption requires sacrifices that could cost her everything: her abilities, her humanity, and ultimately her life. As the network accelerates plans for a continent-spanning "Great Harvesting" that would kill millions, Kira leads desperate resistance fighters through underground passages being transformed into living organisms designed to drain life force from anyone who travels them.
Her only advantages are forbidden techniques that predate the enemy's defenses - and the willingness to pay prices that tradition says no one should ever be asked to pay.