Leviathan Wakes left the protomolecule alive and building on Venus. Caliban's War reopens the wound at Ganymede, breadbasket of the outer planets, where a monstrous protomolecule 'soldier' slaughters a UN and Martian Marine platoon — Bobbie Draper the lone survivor — and the station collapses into war and famine. Beneath the chaos, botanist Prax's medically fragile daughter Mei is abducted from her school by her doctor Strickland. Four threads braid together: Prax's desperate hunt for Mei, which his viral appeal makes a system-wide cause; Bobbie, defecting to work for UN power broker Avasarala, who uncovers a rogue faction under Errinwright and Nguyen building protomolecule-human hybrid weapons with the industrialist Jules-Pierre Mao; and Holden's Rocinante crew, drawn in when they rescue Prax and shelter Avasarala after Errinwright exiles her. Holden, briefly consumed by a fear-driven vendetta, loses and then wins back Naomi as he sheds it. The threads converge on the enemy lab at Io. En route, the crew flip a trailing Martian fleet into allies and survive Nguyen's destroyers; Avasarala's politicking forces Secretary-General Sorrento-Gillis to topple Errinwright. At Io two fleets deadlock until Nguyen, cornered, fires over two hundred monsters at Mars and is undone when one infects his own flagship, the Agatha King, into an Eros-style plague-ship. Holden boards it alone for the transponder codes that let the fleet track the swarm — executing the bargaining Nguyen, and losing the sailor Larson, who sacrifices himself to detonate the ship. On the surface, Bobbie meets the monster of her nightmares and burns it down with incendiary fire; Amos and Prax fight into the lab, find Mei alive, healthy, and grown, and Amos executes Strickland when Prax, holding his daughter, refuses revenge. The war won, the crew ride home to Luna: Avasarala inherits Errinwright's vast power and 'erases' the captured Mao; Bobbie chooses to live, going home to Mars; Prax accepts leading Ganymede's reconstruction. Then the protomolecule finishes its billion-year work — a glowing tentacled structure larger than Ganymede rises from Venus, scatters the watching ships, and flies off into the void under no visible drive. In the Roci's galley, Holden, terrified less by an ending than by an incomprehensible beginning, is confronted by the impossible apparition of the dead detective Miller: 'Hey. We gotta talk.'