In the aftermath of the raid, the cultivator cadets visit Kieran’s grave at the Cartwright’s ancestral cemetery outside the city of Androscoggin. Mackenzie admits to Isaac that he has a point about revenge and justice, and will keep quiet about his desire to overthrow the junta for the time being.
Back at the Elizabeth Pond military base, Stockham explains to Isaac and Babs that he’s trying to keep his position amid a power struggle among the junta - the State Police and Army, allied with each other, wanted to appoint Vice Commandant Spinelli of the Naval Police to become the new head of the Cultivator Marines. However, Secretary Ricci of the Navy, along with his subordinates - Admiral Broadhurst of the Combined Fleet and Commandant Firmino of the Naval Police - distrusted Spinelli and got Stockham, a bureaucrat within the Naval Bureau of Metaphysical Research, the job instead. Many of the Cultivator Marines support Spinelli, forcing Stockham to rely on his own cadets for missions. With the support of the State Police and Army, Spinelli’s Naval Police take Sam into custody, arguing that the Cultivator Marines have no authority to investigate any conspiracy beyond smuggling. Mr. Cartwright arrives and reveals he’s in league with Spinelli, threatening to use his son’s death as a means to advance their own plans for power.
Babs admits to Isaac that she tried to kill Sam exactly for this reason - once he's in the hands of the Naval Police, there’s no telling what would happen to him. According to her, sometimes justice is death. While Isaac stews on that, they visit Reed, who’s been in a slump since having her memories exposed. Babs manages to cheer her up with some philosophy; Reed says she’s been afraid to want anything since her family always told her she should only want to be a strong cultivator. But now she knows that it’s okay to want, and she decides she wants to be somebody…Reed, the movie star! And after hearing about Karin’s obsession with God, Isaac recalls the message in his brother’s original notebook about humanity trying to seize the kingdom of heaven from Him five hundred years ago.
While out on a naval patrol with Dan and Demetrius, Isaac comes across a dead Atalantan refugee in the water, washed out to sea from the massive sewer pipes below the city draining into the bay. Upon returning to the base, they discover Sam died under Naval Police custody; according to Spinelli’s son Henry, the truck driver from the Machigonne raid murdered him before killing himself. Officer Connor of the Naval Police confronts Isaac that night, revealing he’s been giving random room inspections in an attempt to find Greg’s journal page on behalf of unknown backers. With both the Restorationists - via Sam - and the State Police/Army/Naval Police - via Connor - having tried to steal his journal page, Isaac suspects that all of the above factions are working together in some capacity as part of a grand conspiracy.
Henry Spinelli, who possesses the ability to change the volume of any object with just a single touch, murders Connor, declaring that the officer worked together with the truck driver to kill Sam. He and his father threaten to arrest Isaac, but the intervention of Mackenzie and later Stockham saves him. Isaac reveals his theory about the conspiracy to Reed and Babs and, with just how outnumbered they are, suggests they go to Stockham with the information for support; Reed rejects this, preferring to run from her problems, even after Isaac points out that the Dr. Oswald who lobotomized Karin is the same doctor whom the State Police brought Kassandra to. Babs rejects Isaac’s proposal too since she feels they can’t trust Stockham.
The next morning, however, both women agree to the plan - Reed’s tired of running while Babs admits they’ll need a united front to fight the conspiracy. Stockham agrees with their assessment, then speaks to Isaac alone. The reason the squads were ambushed at Machigonne was because one of the squad members somehow warned Machigonne in advance of the raid. Aka - of the people who knew about the mission, one of them is a traitor. By pinning the murder of Sam on the truck driver, the conspiracy wanted them to think the truck driver was the traitor. But the job was sloppy, with the truck driver being clearly murdered rather than killing himself as alleged. Therefore - one of the members within Squads 1, 2, and 3 must be the traitor who informed Machigonne in advance.
Feeling dazed by the revelation, Isaac visits Lynn. Having been severely rattled by having her memories exposed, she demands Isaac find a way to prove their friendship. He’s unable to, so he leaves and cultivates until he unlocks the Knyzosis Perception Art. Deciding to trust in Reed, Isaac reads the journal page with her, which indeed has encrypted writing rendered invisible to anyone who lacks Knyzosis. The page describes a Project Patmos whose goal it is to restore mankind to the Garden of Eden, along with other esoteric writings such as nearly a billion souls in a Tree, the Heart, the Mind, and the Soul, and a warning to beware the Mark of Cain. Isaac tries to connect the Garden to the Gardener, but like always, his memories of her escape him.
Reed relays the first few chapters of the Book of Genesis to Isaac, explaining the current Arcadian religion with its Skyfather is just a transformation of a pre-Unleashing religion. Reed identifies the Mark of Cain - an octagon with a line diagonally running through it - as the symbol of the Sect Hidden in the Mountains. This unsettles her, because the Sect should’ve been destroyed fifty years ago. Isaac fears that the survivors of the Sect might’ve infiltrated the Arcadian government since one of the survivors, Derek Domino, is allegedly still alive as a hermit. Reed flatly denies such a possibility because Domino was none other than her final tutor who passed down his sword to her and helped her run away from her family to the Navy.
Stockham only reveals his next mission to Isaac and Reed. While Sam was murdered in custody, the surviving office workers are still alive, and revealed to Stockham that much of Machigonne’s workforce came from the Narragansett ghetto of Four Eagles. The land and buildings of the ghetto had been purchased from Zhanghai, with many of its inhabitants evicted and forced into contracts with Restorationist shell companies afterwards. Reed goes through all of Zhanghai’s real estate purchases made after an official named Dai Hong was appointed head of its Arcadian division; she discovers that not only does Zhanghai own the Fore River dockyard where the Melusine once smuggled in goods, but they own the land over every subway station of the pre-Unleashing city where Narragansett now stands. With Zhanghai now linked to the conspiracy, Isaac and Reed deduce that the samurai allow the Restorationists to smuggle goods through the city using the subterranean tunnels, with the nerve center of the operation being a pre-Unleashing stadium now buried beneath Four Eagles.
The office workers also reveal a brilliant set of twins - the Dedericks - had been working on a project for Zhanghai in Four Eagles, but recently fled to a safehouse within the ghetto. Isaac navigates the ghetto, surviving an encounter with local triads led by the Atalantan refugee Lysandros, whom Isaac spares. He then discovers that Zhanghai already found and murdered the Dedericks, but have been unable to break into a safe within their hideout. The ghetto’s top boss, Zou Mei of the Restorationists, will be in town tonight to break the safe herself, so Isaac races there first. Isaac unlocks the safe with the Knyzosis Art, finding technical documents inside. The Dedericks were loyal to the Restorationists, and transformed the Zhanghai project - known as Polyphemus - into a weapon for them. The weapon would be powered by something called the Heart, something so terrifying that it drove the Dedericks into hiding.
Isaac struggles to find a connection between Viola Reed, who invented the Art, and the Restorationists who now use it. He also struggles with Zou Mei, who’s arrived with corporate samurai allies. Isaac narrowly escapes by blowing up a bar with her inside it; she survives, as does Isaac, who’s escorted out of the ghetto by Lysandros. Grateful for sparing him, Lysandros explains that many Atalantan refugees have been enslaved below ground by Zhanghai and the Restorationists, and then asks Isaac to use his cultivation to change this country for the better; Isaac agrees. Back at the base, Stockham has his head researcher, a woman named Essex from the Naval Research Bureau, go through the documents, while Isaac recovers. Lynn visits him and forcefully confirms their friendship, since he’s helped her realize that she should escape life as a cultivator by dying in a blaze of glory.
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Stockham and Essex take Isaac to a facility below the base and show him the Heart, a pre-Unleashing biomechanical device as big as a building and shaped like its name. A convict is sacrificed to the Heart, which absorbs both his blood and Rddhi. Essex suspects the Heart was once used as a battery, with sacrifices as its fuel. The Heart’s remained alive for five hundred years through a process similar to photosynthesis except that it specifically requires moonlight rather than sunlight. The Restorationists are after the Heart so they can use its battery power to fuel the Polyphemus weapon, a process facilitated by the atomic material smuggled inside Arcadia. Stockham plans to use the Heart as bait to defeat the Restorationists once and for all. Isaac, meanwhile, realizes this is the Heart Greg referred to in his cryptic journal page, and wonders if there’s a Mind and Soul out there as well.
Stockham works with a surprisingly agreeable Dai Hong to concoct a cover story to draw the Restorationists out into the open. The Navy will use Zhanghai railroads to dispose of “pre-Unleashing atomic waste”, hoping the Restorationists will deduce it's a cover story for transporting the Heart above the ground so it may receive moonlight. In the days before, Isaac and Reed discuss the Greeks, whose philosophy inspired the Restorationists. Reed explains the concept of Kallipolis and the philosopher-king. Isaac realizes that when he overthrows the junta, he wants to create a country based on freedom; Reed answers that it’s much easier for the starving, illiterate masses of Arcadia to desire trading a bad dictatorship for a good dictatorship than some abstract concept like a free society. Babs also shows Isaac her new power - the ability to use her wind to throw an impenetrable shield at the cost of cutting off a finger. In a tender moment, she admits she’s scared that tomorrow’s mission will be their last. And if it is their last, if one of them should die, the other needs to keep fighting to change the country.
Squad 3 is posted on a train with Lieutenant Derry and his conventional marines of the Combined Fleet. They do indeed come under attack from Restorationists initially led by Zola, the preacher who was captured by the State Police during Isaac’s first night in Narragansett. He uses the Reverse Spiral - a technology only known to the State Police - to ambush the train. Reed successfully destroys the spiral and kills him, but Zou Mei arrives with reinforcements and disables Reed by burning half her face off. Zou Mei, with her magnetism ability, defeats both Babs and Isaac, only to discover that the Cultivator Marines weren’t transporting the Heart at all and she indeed fell for the bait. With Isaac at her mercy, she explains that Dai Hong once came to Arcadia as a minor official years ago; when he returned to Zhanghai, he left behind Zou Mei, his young illegitimate daughter. When he returned to Arcadia as head of the Zhanghai Industrial Corporation there, they brokered a partnership between Zhanghai and the Restorationists. Before Zou Mei can kill Isaac, the wounded Reed shoots her. Naval reinforcements arrive, so Zou Mei flees with the Restorationists in defeat.
Back at the base, Isaac confronts Babs, having deduced that she's been the traitor all along, having killed Panama during the raid on the Melusine and alerted Machigonne ahead of time. Babs reveals she's indeed a Restorationist, but there's not one big conspiracy - Isaac is fighting a whole host of them, all competing with one another for control of Arcadia. Babs' leads a conspiracy of junior officers within the various factions tired of all the politicking; Isaac and Reed refuse her offer to join her. Before they can capture, a cultivator with the power to turn into a giant attacks the base and steals the Heart. Isaac fights Babs, only to be defeated and left for dead. Isaac finds himself in an illusion spell that reveals Babs' backstory - she was once a triad who became a hardcore Restorationist in service of Caesar, the man leading the movement. However, the discovery of Caesar's murderous methods, as well as his execution of her mentor when he learned the truth, causes her to concoct a plan to lead the Restoration of Kallipolis with herself in charge. Allying herself with Zou Mei, Henry Spinelli, and a junior officer within the State Police, Babs plans on stealing the Heart to power Polyphemus and seize control of the country. Isaac realizes the State Police junior officer is the giant, and rescued him from death for reasons only known to herself. The officer identifies herself as the Mind, created by the same makers of the Heart, except she at least has a consciousness.
The Mind flees, and when Isaac is brought back to the base, he reveals what he's learned to Stockham, Broadhurst, and Firmino. The State Police, meanwhile, have pinned the giant's rampage on Zhanghai Industrial Corporation, and Chief Amien announces that all Zhanghai assets within Arcadia have been nationalized. As the race for control of Zhanghai assets among the junta branches begin, Henry Spinelli attempts to assassinate the Naval leadership, only succeeding in killing Firmino before being captured. Firmino's death makes Vice Commandant Spinelli the acting leader of the Naval Police; he compromises by allowing Isaac and Reed to come under Combined Fleet custody. Reed, finally feeling comfortable with who she is, rallies a broken Isaac; both of them reach Circuit 2A, and Reed unlocks the ability to use magnetic waves with her Domino Sword.
When the Naval Police come to collect them after all, Dan and Lynn swap places with Isaac and Reed, enabling them to escape and meet up with Lieutenant Derry. Narragansett comes under fierce street fighting, especially in Four Eagles, where the State Police attempt to storm the ghetto and reach the stadium facility, which is now under the control of the junior officers. Derry takes Isaac and Reed out of the city; Chairman Dai Hong, under attack from his own mutinous junior officers, promised to reveal a secret entrance to the facility in exchange for his safety. Isaac and Reed make it to his estate, which comes under attack from Zou Mei. Dai Hong shows the two a secret subterranean minecart track from his estate to the stadium, along with giving Isaac his ancestral Bracer of the Westward Wind, before Zou Mei mortally wounds him. Reed then defeats and kills her; father and daughter reconcile before passing.
Taking the track, Isaac and Reed storm the stadium facility below Four Eagles just as the State Police break through. Babs activates Polyphemus, revealing it to be an airship with a superweapon attached. As Polyphemus takes off, Isaac and Reed climb aboard and confront Babs, who's leading an entire aerial armada to destroy the government in downtown Narragansett. The superweapon is a giant cultivation laser; Babs destroys the headquarters of the Bank of Arcadia and then targets junta headquarters. The State Police fires land-based missiles, a previously hidden technology, and the sudden attack gives Isaac and Reed a chance. Reed slays the technicians while Isaac fights Babs for the last time; when she activates her Whirlwind Reaper, he defeats her by just using his unpowered fists. Isaac then uses his superpowered punch to deliver the final blow, which destroys her heart. Reed thanks the dying Babs for helping her on the rooftop when she was feeling down; Babs reminds Isaac of his promise to keep fighting to change the country. Babs dies, and Isaac and Reed escape using Reed's magnetism as State Police missiles destroy Polyphemus, bringing the attack to an end.
Their escape costing them both broken legs, a wounded Isaac and Reed regroup with Stockham and Broadhurst days later. In retaliation for the nationalization, Zhanghai has announced a full embargo of Arcadia, which will cost it much needed food and fuel resources for the upcoming winter. The State Police have used the violence to tighten their own control of the country, including indefinite martial law. While Babs' identity remains a state secret for now, the State Police and Army have successfully used its control over the media to credit themselves with victory over Zhanghai and the armada. But on the bright side - the Navy has increased its own power by seizing a Zhanghai rail depot, the Fore River dockyard, and have welcomed many former Zhanghai officials and cultivators with their knowledge and expertise into its ranks. Furthermore, Isaac and Reed get a holiday bonus and though they'll remain watched by the Naval Police, they'll be freed from house arrest for their service. And on top of all that - Squad 3 is officially renamed as Squad Reed!
Isaac and Reed finally reunite with his friends. Though a dark storm is brewing across Arcadia, Isaac feels confident he'll weather it. The Gardener then appears to him, showing him what must be the Garden of Eden, and Isaac wonders if the Gardener is Eve and he's Adam. The Gardener tells him to take care and the vision ends. Isaac decides to enjoy this night with his friends - and we're onto Book 2.