In the wake of the disaster on Eros, the crew of the Rocinante is forced to regroup and recuperate ... including Joe Miller, who's been brought into the fold. The Roci crew is a bit traumatized by what they saw on Eros, and they vow to hide the piece of the protomolecule they took amid an asteroid field until they know what to do with it.
Meanwhile, tensions between Earth and Mars continue to escalate. An armed stand-off near Phoebe research station is a chance for Undersecretary Chrisjen Avasarala to flex her diplomatic muscles, but the Martian ship doesn't fire on the Earth vessels. It fires on — and destroys — Phoebe station.
After returning to Tycho station, the Roci crew and Fred Johnson come up with a plan to overtake the research station where the data from the Eros experiment was being beamed. Once there, they unhook one scientist, the emotion-less Cortazar, from a neural network and come upon Dresden, the man who was overseeing the abomination on Eros. Fred wants to bring him back to Tycho, but Miller instead shoots him dead.
With Earth/Mars tensions escalating, Martian gunnery sergeant Bobbie Draper is spoiling for a fight, though her commanding officers try to keep her patient and disciplined. When Earth retaliates for the Phoebe incident by blowing up the Marian moon Deimos, Bobbie is ready for payback.
With Eros still teeming with protomolecule activity, Fred and Miller come up with a plan to knock Eros on a course into the sun by ramming the Mormon ship Nauvoo into it. The plan appears to be working perfectly — until Miller ends up stuck on Eros while trying to set charges. The collision with the Nauvoo never happens, though, because Eros, powered by the protomolecule, moves out of the way.
The movement of Eros all on its own shocks the galaxy, with neither Earth nor Mars nor the Belters on Tycho prepared for what to do about it. When Eros takes on a collision course with Earth, panic sets in. Earth launches a massive arsenal of nukes towards Eros, but Eros manages to vanish from radar. Fred Johnson reaches out to Avasarala through backchannels and offers to guide the missiles himself, if the UN will trust him. So Fred gets control of the nukes, but Eros continues to speed faster than Fred and the Roci crew can keep up.
Miller is still stuck on Eros, though, so he's able get inside, through corridors thick with protomolecule, and gets to the center, where Julie Mao is being animated by the protomolecule. It's she who is controlling Eros' course. Miller has a sweet, sad last moment with Julie, as he convinces her that she has to change course. He's successful, and Eros, Miller, and Julie all crash into the surface of Venus instead, saving Earth and (one assumes) killing Miller in the process.
Back on Tycho, Fred Johnson suddenly finds himself in possession of an arsenal of Earth missiles, which ought to make for quite a bargaining chip. At the same time, Holden and the Roci crew agree that they must destroy their sample of the protomolecule, for everyone's good. But unbeknownst to anyone else, Naomi changes the coordinates and stashes the missile where no one will find it.
On the jointly-occupied Ganymeade agricultural station, Bobbie Draper and her crew patrol the Mars/Earth border when suddenly they see UN troops running towards them. They mistake it for an attack and fire back, which sets off a conflict between the UN and Mars above, resulting in Ganymede station being nearly destroyed. Bobbie's whole team is killed and before she passes out, she sees a figure standing over her without a space suit.
While Avasarala struggles to keep Earth and Mars from armed conflict in the wake of the Ganymeade attack, Bobbie must cope with the news of her dead team. She tells Martian officials about what she saw — a drone overhead just before the attack, and of course the figure without a space suit, which she realizes was chasing the UN forces which made Bobbie's team think they were attacking. But she's told there's no evidence of this She's to attend the Earth/Mars summit in New York and testify (falsely) that her team fired first in order to prevent a Earth/Mars war.
Meanwhile, on Tycho, Anderson Dawes arrives from Ceres to help deal with the influx of refugees from Ganymede. Already a Belter hero, Dawes is able to rally the Belters on Tycho, subtly turning their minds against the Earther, Fred Johnson. When Dawes discovers that Fred has a scientist onboard with knowledge of the protomolecule — which Dawes can use as a weapon against Earth and Mars — Dawes is able to abduct Cortazar and escape.
One survivor of Ganymede is Dr. Praxidike Meng, a botanist who fears his daughter — who was off at a doctor's appointment at the time of the attack — has been killed. After Prax is witness to the belters on his rescue ship blowing Martian survivors out of an air lock, he's traumatized. He ends up on Tycho station, which is a coincidence, since ...
... Holden and Naomi pick up on a protomolecule signal coming from Ganymede. The only ProtoGen connection they find in the Ganymede records is Dr. Lawrence Strickland ... Prax's daughter, Mei's, doctor. So Holden and Naomi find Prax and after telling him about Strickland and Mei, he begs then to take him onto the Rocinante in their search for Strickland.
Meanwhile, there's an attempted coup as Belter agitators attempt to remove Fred Johnson from power. The Roci crew is able to quell the uprising, but when Holden and his crew leave to search for the protomolecule, Holden and Fred leave on tense terms.
In order to get onto Ganymede, the Rocinante crew commandeer the relief ship the Weeping Somnambulist. They're able to get to Ganymede, but in an ensuing shootout with gangsters on the ground, the husband of the Somnambulist's captain is murdered. Naomi is badly shaken up by this.
Her Martian superiors upbraid Bobbie for her testimony in bringing up the man without the space suit. Before she can be sent back home, though, Bobbie escapes the embassy and seeks out the waterfront. There, she's met by Avasarala, who shows her intel she's gotten about Martian plans to weaponize the protomolecule in the form of a hybrid creature that looks exactly like the figure Bobbie saw on Ganymede (Avasarala got these from her boss, Errinwright, who turned them over when Avasarala busted him for being part of a conspiracy to get his hands on the protomolecule).
Bobbie is then dragged back to the Martian embassy, where she's told that she's never going to be a soldier again AND learns her unit was knowingly sacrificed to test the rotomolecule hybrid. After Bobbie escapes again, she makes a run for the Earther guard post and declares that she's seeking political asylum.
The Roci crew (with Prax) search Ganymede for Dr. Strickland and Mei. Instead, they find a chamber with children cryogenically frozen inside pods and then a room full of scientists. There is a shootout, followed by an attack by the protomolecule hybrid, with one of the doctors telling Holden that they molded the protomolecule in man's own image, before she dies.
After the shootout, Naomi tells Holden she can't keep going down the path they're going. She re-joins the Somnambulist and tries to evacuate the remaining Ganymede survivors. There are too many to fit on the small relief ship, though, and she has to struggle to convince the belters to not riot as they board.
Meanwhile, Holden, Prax, and Alex aboard the Rocinante are hunting the protomolecule hybrid that they saw during the shootout. Holden is getting maniacal in his need to eradicate this weapon, even as Prax worries that the creature could be Mei after she was experimented on.
Holden and Naomi are reunited aboard the Rocinante, and Holden's mania has subsided some. Only now the hybrid has gotten aboard the Roci, and our crew needs to kill it before it kills them. Holden almost dies as the attempt to overtake the creature. The only solution is to lure it outside of the ship with a nuclear missile and then roast it. Which they do.
Meanwhile, Avasarala (along with her right-hand man Cotyar as well as Bobbie Draper) answers a summit request from Jules-Pierre Mao, who by this point has gone into hiding after having been exposed as the man behind the protomolecule experiments. When the two begin to bargain, they're interrupted by a message from Errinwright, who informs them that he's murdered a Martian official and destroyed a Martian ship on Ganymede. He tells Mao to return and resume their partnership ... and to murder Avasarala, who he feels has betrayed him (and is the only person that can expose him). Avasarala and Cotyar are under fire from Mao's men, but they're saved at the last minute by Bobbie, who cleans house.
Meanwhile, the research ship that Earth had sent to get data readings from the Eros crater on Venus attempts to drop closer to the surface — since other readings near the crater have proved impossible. Just as the ship approaches the crater, it is pulled apart by the protomolecule, which seems to have survived its crash landing on Venus just fine.
Finally, Naomi admits to Holden that she never fired that rocket of protomolecule specimen into the sun. In the hopes of giving the Belt a fighting chance against Earth and Mars, she gave the protomolecule to their old friend Fred Johnson.