A 15 year-old Belter operative named Filip and a small team infiltrate the twin Earth/Mars shipyards on Callisto to steal canisters of High Density Resonance Coating, Stealth tech used on Martian military ships. They have a ship in orbit called the Pella that releases tungsten slugs to take out the Martian ships in orbit, as well as the Martian marines in power armor on the surface. The team suffers a few casualties but manages to escape with their loot--just as their ship launches a rock into the moon.
A year after the Callisto attack, 6 days after they got back from Ilus, the crew of the Rocinante arrive at Tycho for repairs--the new chief engineer Sakai (R.I.P. Sam) estimates they'll take around 6 months. Alex doesn't like how he left things with his ex-wife (they were happily married and had their own place after he left the MCRN, but he wanted to keep flying) and plans to visit her on Mars. Amos needs to head back to Earth because a woman he knows (Lydia, the face of whom he has tattooed on his chest) has died. Naomi wants to hire more crew since in case anything happens to any of them. She gets a call from someone in the OPA telling here that Filip is in trouble.
Fred tells Holden that he's headed to Medina Station, as that's where all the power is. He and Avasarala are back-channeling a lot of the dealings, but Fred's concerned about all the offshoot branches of the OPA; with all the new planets, life on the space stations is going to die out, but the Belters aren't all physically capable of living on the planets. Apart from Callisto, they made an attempt at attacking Earth as well.
Namoi tells Jim that she needs to go to Ceres, alone, and that he needs to let her go or they'll have to break up. She leaves, and Holden is completely alone for the first time in years. Later, he gets a call from journalist Monica Stuart, who is also on Tycho, and she asks to meet up. Over dinner, she shows him a video of a freighter that went through one of the rings and then disappeared.
Alex visits his wife Talissa when he gets to Mars, but she angrily tells him to go. He gives Bobbie Draper a ring to see if she wants to meet up, and she agrees.
Upon arriving in New York, Amos is promptly "arrested" and taken to an interogation room at the police station. Chrisjen Avasarala greets him via TV monitor and asks him what the fuck he's doing on Earth, if Holden sent his "hired killer" to take out Murtry or something. Once he assures her he's there on a personal errand, he's free to go. Amos looks up Lydia's obituary and finds that her husband Charles was the last to see her alive; Amos goes to meet him.
Monica informs Holden that the Rabia Balkhi is only 1 of 13 ships that have disappeared after going through one of the Rings, and no one is talking about it. She somehow knows about Fred's sample of protomolecule and wants to use it to consult proto-Miller; Holden says no way, and thinks maybe the OPA is involved in the disappearances. He broaches his theory with Fred, who tells him "no way" and that he should drop it.
On Ceres, Naomi meets up with an old friend, a massive Belter called Cyn, who takes her to see Filip, Naomi's son to Marco Inaro. Naomi left Marco after he used a program she wrote to sabotage the fusion reactor on the ship Augustín Gamarra, killing 234 people; this was the initial OPA rebellion, after the UN shut down the proposed Belter homeworld, Terryon Lock, in the Jovian system. Afterwards, she tried to kill herself. Marco told her to leave and not to come looking for him or Filip.
Filip wanted her to bring the Roci to take to the Hungaria cluster where they have a ship called the Pella. With the Roci still being repaired, she charters a ship covertly with Outer Fringe Export (who Holden had almost taken a job for back before they went through the Ring).
Amos heads to Philly and meets up with Lydia's widowed husband, Charles, who turns out to have been an OK guy that truly loved her--so Amos doesn't kill him. Charles knows Amos as Timothy, and Lydia was Timothy's surrogate mother after his biological mother died. Charles says that with Lydia gone, he can no longer afford the house, which was being floated by some gangster named Erich.
Amos goes to visit Erich in Baltimore; Erich used to be a small time hacker, he has one tiny little arm and one regular one, and is now running the streets that he and Amos used to work. Erich says he treated Lydia very well, but Amos insists he take care of Charles too. Erich agrees, so Amos says he won't kill him. Erich is grateful, but tells him there was a flechette turret hidden in the ceiling. Before Amos leaves Earth, he calls Avasarala and asks her to let him see Clarissa Mao, who he became fond of when they escorted her as a prisoner.
Alex goes to visit Bobbie. She's been investigating the sources of black market military equipment leaving Mars for Avasarala, and she asks Alex if he'll help her by talking to some of his buddies in the MCRN; he says he'll think about it. Before he leaves Mars, he visits Bobbie again one more time with the intention of telling her "no, he can't help", only to find a small group of men have broken into her house and tied her up. He calls for emergency services, then rushes in to save her. He gets stabbed and she gets shot, but they survive. Bobbie tells him the men were there looking for him. He says he'll stay and help her.
Holden pays a "data wonk" called Paula Gutierrez to write him a program to find any ships that may be suspicious. When he tells Monica, she's upset that he's brought Fred, Sakai, and Paula in on the investigation, especially since they're all OPA. The next day, he gets a hit on a ship called the Pau Kant located in the Hungaria asteroid group that is relatively close to Earth and Mars. He calls Alex and asks him to check it out before he comes back, then tries to track down Monica again--but her room on Tycho has been ransacked and she's missing. He warns Fred that he's got OPA radicals on the station.
Alex and Bobbie make it to the hospital and survive their respective surgeries. Bobbie reasons she was attacked because via the Roci, Alex is involved with Mars, Fred (OPA), and Avasarala (UN). Bobbie says that while the Donnager class warships are well tracked, the corvettes they carried were less so, and with all the battles lately, they were turning up and disappearing quite a bit if you looked at the data properly. Someone high up in the Navy would have to be involved for the level of clearance required in overwriting the records; that's what she wants Alex to look in to, while she looks into who hired their attackers. Alex gets Holden's message about checking on the ship in the Hungarian cluster; Bobbie says Avasarala gave her Julie Mao's ship, the Razorback, and that he can use it.
Holden and Fred check the security footage and see 2 guys (not in Tycho's system) in jumpsuits and caps go into Monica's room and leave with a shipping crate. They go to the dock and find the crate but it's empty, meaning someone must've edited the security footage. Fred puts the station on lockdown. Back in Monica's quarters, Holden finds that her phone seems to be receiving a signal from the hidden camera she wears for interviews. They track her to a sealed cargo crate and find her inside, drugged and tied-up, but mostly unharmed.
Alex meets with one of his MCRN buddies who hooks him up with a Commander Duarte; he too has noticed the missing ships, even the same one Alex is tracking, the Apalala. Duarte tells him that the tracking of supplies, ships, and material has collapses and they have no idea what all they're missing. He tells Alex to meet up with a programmer named Karlo that first noticed the discrepancies in the database; Alex goes to his place only to find him dead. Alex asks Bobbie to go check out the asteroid Holden told him about, and she agrees to come with him.
Fred gets in touch with Anderson Dawes, another OPA bigwig, who points him towards chief engineer Sakai. Fred interrogates Sakai, who spills that he was involved; he skirted around Fred because he's racist against Earthers, even if Fred is OPA through and through. Fred punches him out and throws him in the brig.
The ship Naomi purchased is called the Chetzemoka. When it's ready to board, she pulls Filip aside and tells him she can't come along on their mission, but that she wants him to have the ship, and that afterwards, there's a spot for him on the Roci if he wants to come with her. The giant guy, her friend Cyn, puts Naomi in a bearhug while Karal sticks her with a needle full of sedatives.
When they get near the Hungaria cluster, Alex realizes that they're being painted with a targeting laser. He makes some scans himself and gets ping after ping of Martian corvette class ships running dark. The ships let loose a couple of missiles and Alex takes off at 10gs towards Luna, where the Martian Prime Minister has a convoy, hoping they can make it in time for the PM's ships' PDC cannons to take out the missiles. Alex kicks it up to 15gs and it rips the wound open in his stomach. Before he passes out, he jettisons the core and it crashes into the first of the missiles; the Martian PDCs take out the other.
Naomi is taken to the Martian corvette where Marco is. He tells her he brought her there to keep her safe, because she's one of them--but she's pretty sure he really just wanted the Roci. Ostensibly, the attack they're planning is because the Earthers are abandoning their entire race to die, since Belters can't survive in planetary gravity. A racing ship arrives at their location (the Razorback) and Marco says to destroy them. Naomi is locked up and forced to watch the newsfeed of Marco's assault on Earth.
While Amos is in the waiting room to see Clarissa Mao, the news reports that an asteroid hit somewhere in South Africa, causing tremendous damage. Guards take Amos to Clarissa's underground cell, and he tells her about all that's happened with the Roci since they dropped her off. In the middle of his story, the place goes on lockdown; a guard tells them that multiple other accelerated rocks have impacted around the globe, causing massive destruction worldwide. The rocks were undetected because they were coated with stealth coating.
On Tycho, Fred and Holden are watching the news when 3 people enter the office and start shooting. Fred is hit, but he and Holden manage to kill/fend off their attackers; however, the station's defense grid is disabled and someone fires torpedoes at them. One torpedo hits and cracks the drive cone. Fred and Drummer coordinate an attack on the intruders in engineering and regain control of the station. A second torpedo with a salvage mech on the end impacts Fred's office; it escapes with the protomolecule sample.
Amos convinces the guards they need to get out of the prison before the building collapses, and they reluctantly agree. With the help of a prisoner called Konecheck, who has enhanced strength like Clarissa's, they manage to crawl up the elevator shaft to the surface. Konecheck kills a few of the guards and injures Amos before Mao shoots him and Amos kicks him down the elevator shaft. The surface is totally devastated and the sky is so dark with debris that Clarissa mistakes the sun for the moon. Amos suggests they walk to Baltimore because he knows some people that can get him to Luna.
Naomi tells Filip that after Marco made her kill, she wanted to kill herself; she tells him to come find her when the remorse of killing a quarter billion people sets in. He tells her she's merde to him.
Alex and Bobbie meet with the Martian Prime Minister Smith while they convalesce. They debrief for hours; mostly the Martians are glad Alex and Bobbie intercepted the hidden fleet, or things could've been even worse; they're still a bit suspicious though. Six and a half relief ships are en route; one of them is the Chetzemoka however, the ship Namoi gave to Filip.
Fred Johnson asks Holden to take him to a meeting on Luna with the Martian PM and Avasarala, who is now head of the UN. Fred plays Holden a message he got from Anderson Dawes, asking Fred to join with the new faction of the OPA; Holden is appalled, but Johnson is actually considering it--that's the side that's in charge now, and Fred can't decide if he should declare against them or stand beside them and help control the fall. Medina Station goes dark, and Drummer reports 25 Martian ships are en route to it.
Naomi asks Marco if he brought her aboard just to show off; he reiterates that he brought her there to save her, and to get closure. She insists it's because he's jealous of Holden, which infuriates him and he says he might kill Holden. She says he can't do anything to Jim, and he tells her that maybe she will. She pieces things together and realizes Sakai must've used her sabotaged the reactor driver on the Roci.
Amos and Peaches (aka Clarissa Mao) kill some doomsday prepper and load up on weapons, supplies, and a couple of bicycles. They walk to Baltimore and meet up with Erich, then proposition him to go to Luna with them, by way of a private launch pad on Lake Winnipesaukee. At first he's incredulous that they'd ask him to abandon his territory, but when Peaches breaks his wall of denial and he realizes he's got nothing left, he agrees.
Alex, Bobbie, and the Martian PM are forced to flee their Martian convoy in the Razorback when the relief ships turn out to be OPA-controlled; they attack and board the Martian ships without much resistance. The Razorback, accompanied by about 100 Martian missiles flying in tandem alongside them, make for Luna with the OPA ships in pursuit.
During the battle with the MCRN convoy, Naomi breaks into an access panel and broadcasts a message to Holden warning him that the Roci's fusion driver has been sabotaged with bad code. Marco tells her that since she sabotaged his plan, which was only to shut the Roci down, not destroy it, that now she's forced his hand. He plays her a faked distress call in her voice, asking Holden to come save her. On the way back to her cell, she stops at the med bay and starts a kerfuffle there, during which she manages to pocket an emergency decompression kit, which should cycle the airlock on the Chetzemoka.
Holden gets Naomi's message just in time; they shut down the drive at 60% and reload a new driver. His hired programmer Paula finds the bad lines of code in the sabotaged driver and tells him that when the reactor hit 95% it would've lost containment and taken most of Tycho Station with it. She realizes this could've been what happened during all the reactor accidents in the past, meaning they were all murders. Holden, Fred, and a crew of Tycho workers depart in the Roci, leaving Drummer in charge of Tycho.
Marco issues a statement from the Pella, declaring himself the commander of the Free Navy and saying that Mars and Earth no longer control anything outside their respective planets. He calls for everyone from the Belt and the outer planets to rise up and follow them.
Amos, Erich, Peaches, et. al make their way to the Lake where the shuttles are. They find one named the Zhang Guo, but it needs repaired, and there's a tribe of people trying to shake them down; Amos beats the shit out of one of them, then Amos et. al. start repairing the shuttle. Just as they're doing final testing on it, the tribe returns with many more people and many more guns. Amos's group manages to stave them off long enough to launch the shuttle. They successfully make it past the Luna patrol defenses after Amos name-drops Avasarala. Erich offers to let him run the crew, since he's now totally out of his element, but Amos just wants to get back to the Roci. Clarissa is afraid they're going to send her back to jail, but he assures her that there is no jail to go back to.
On the Pella, Naomi escapes from her handler and makes it to an airlock, intending to escape to the Chetzemoka without an EVA suit. Her buddy Cyn comes after her, thinking she's going to space herself, but she sorrowfully blows the airlock anyway, killing him--and hopefully convincing the others she died as well. She just barely makes it to the other ship in time and opens the airlock with the emergency decompression kit she stole earlier. She finds that the ship has been mostly stripped bare, all access panels are locked, it's broadcasting a faked message saying she's aboard and needs help, and it's set to blow if anyone gets close to it. She starts pulling wires and turns one of the thrusters off, making her go in circles; she also short circuits the faked message, making it say "this is Naomi Nagata and I am--in control."
Alex gets Naomi's message and takes the Razorback to cautiously investigate. With no way to communicate, Naomi exits the ship through the airlock in a suit with only 5 minutes of air; she uses Belter hand signals so they know not to get close to the ship. Bobbie uses the mag-boots on her power armor to ride one of the Razorback's missiles like a surf board and successfully rescues Naomi. Once safely aboard, Naomi tells them to blow up the damn ship.
Holden rendezvous with the Razorback and immediately gets Naomi to the medbay, since she's suffering from space exposure and plenty of other traumas. They all make it back to Luna and meet up with Amos, who smuggles Clarissa Mao onto the Roci in a cargo container.
Avasarala calls them all together for an announcement: She's going to start a policing task force against the Free Navy, with joint support from the UN, Mars, and the OPA. Naomi is brought in as a prisoner, and agrees to cooperate and tell everything about Marco if she and the crew of the Roci are given immunity for past events not related to the attack on Earth. Avasarala agrees, and they all go for chow. Naomi and Holden head back to their room and she opens up to him about everything. They exchange their pieces of the story in almost casual, conversational tones then fall asleep together.
When Naomi wakes up, she watches the video of the ship that disappeared entering the Ring, the Rabia Balkhi, and wonders what happened to all the civilian ships, since Marco had only acquired MCRN ships. She comes to the conclusion that something in the ring gate is eating the ships.
In the epilogue, the Free Navy is confirmed to have control of Medina Station, and are commandeering civilian ships. Admiral Duarte of the MCRN has taken control of the remaining Martian military ships in an independent initiative of the fleet, ostensibly working with the Free Navy but planning to attack them from the rearguard later. Duarte appears to have the protomolecule sample and another much larger alien artifact. A Donnager class ship called the Barkeith goes through the Laconia ring; the crew experience a sensation like they are clouds and can see the spaces between atoms. A solid, fog-like alien presence appears on the ship and kills the crew.