Mendoza is a Preserver for The Dr. Zeus Company, living in the past to collect species for the future. But when she kills six people in California in 1863, The Company makes her disappear.

Joseph, a senior Preserver, loves Mendoza as the daughter he never had. Drunk on chocolate and fueled by rage, he's determined to find her however long it takes. Being an indestructible, immortal cyborg gives him an unlimited well of patience.

What begins as a rescue mission uncovers a conspiracy stretching across fifty centuries of recorded history. Behind it lie genocide, graveyards filled with Company agents, and the roots of the ominous Silence that falls across the world in 2355.

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"Sin exists," says Joseph, an immortal cyborg agent employed by Dr. Zeus, Inc., and in this fourth novel of Kage Baker's Company series, it certainly does. The Graveyard Game follows agents Joseph and Lewis as they try to find their missing friend Mendoza, who's been exiled to the Back Way Back as punishment for anti-Company activities.

Dr. Zeus, a time-travel corporation, created cyborgs to selectively preserve artifacts from the past for the edification of the 24th century, when the Company exists. But as the centuries go by for the agents, they hear strange rumors of a "silence" in the year 2355. Ominously, cyborgs who try to investigate disappear forever, hidden away or shut down by Dr. Zeus.

Joseph and Lewis become obsessed with finding Mendoza, and along the way, they uncover evidence of bizarre and dangerous Company deeds. Joseph finds strange underground holding cells, with "retired" agents in vats of preserving fluid. Meanwhile, Lewis researches the activities of Edward Alton Bell-Fairfax, the odd mortal who was with Mendoza when she disappeared. The two get together to discuss their disheartening quest in present-day Ghirardelli Square. Cyborgs get stoned on chocolate, and they order round after round of hot cocoa, even snorting the stuff, until a Company security tech finds them:

On the floor between their respective briefcases was a souvenir bag stuffed with boxes of chocolate cable cars, and the table was littered with foil wrappers from the chocolate they had already consumed.... The security tech scanned them and recoiled slightly at the level of Theobromos in their systems. He surveyed the litter of foil wrappers and empty cups, regarded the cocoa powder in Joseph's beard, and sighed. Two old professionals on a sloppy bender.