Sunny is imprisoned at the Bordo Mines, following his fallout with the River King. There, he’s shackled to a man named Bajie, who discovers Sunny’s secret Clipper identity. Bajie then turns on Sunny by revealing Sunny’s secret in order to receive special favor from the Engineer of the mines. But the Engineer shackles Sunny and Bajie together again and pits them against his burly champion named Mouse for a fight. Bajie and Sunny work together to kill Mouse and flee from the mines.
Ryder becomes Baron after Quinn’s death and inhabits the late Jacobee’s mansion alongside Jade. The Widow orchestrates a massive attack on Ryder’s oil refinery and reclaims her old oil fields.
M.K. trains as a Novice at the Abbot Monastery to practice controlling his chi-enhanced power. He works with an Abbot named Ava until the Master takes him under her own wing.
At a secret bunker, Veil is being held hostage by Quinn, who actually survived Sunny’s attack. She gives birth to Sunny’s baby and names the child after her father, Henry. Quinn rules over the men who stayed loyal after the Fort was compromised. Quinn treats Henry as his own heir.
The Master shows M.K. to a room of mirrors that can elicit buried memories. She sends M.K. into the past where he sees a vision of himself in his dark chi state after having slaughtered Cogs on the River King’s ship. M.K. is forced to battle the dark, empowered version of himself in his visions.
Bajie picks his shackle lock, freeing them both, and decides to follow Sunny to the Badlands.
Veil continues her treatment of Quinn’s headaches, but keeps the status of his growing tumor a secret by using opium-laced concoctions to banish his symptoms.
Sunny and Bajie run into Nathaniel Moon, a legendary Clipper who escaped the Badlands. After initially helping them, Moon demands a battle with Sunny. The two go at it until Bajie slices off Moon’s hand and steals his signature ringed sword. Moon warns Sunny not to go back for his family, for their sake.
After a Novice escapes from the Monastery, he’s brought back and injected with long needles to suppress his gift. M.K. secretly watches.
At the Widow’s Sanctuary, Waldo serves as the Widow’s adviser, while Tilda assumes the role of Regent. While chaos runs amok in the Badlands, runaway Cogs flee to the Widow’s Sanctuary for refuge. Among the runaways is Odessa, a former Doll, who later becomes a Butterfly.
M.K. sneaks into the Master’s mirror chamber. In a vision, M.K. finds his mother covered in blood and realizes he was responsible for her death.
While Quinn is away, Veil drugs a Loyalist named Edgar and attempts to flee, but is caught. She kills Edgar, but finds she’s unable to escape after his key breaks off inside a lock.
One of Quinn’s Loyalists, Gabriel, sneaks into Ryder’s mansion and grants Quinn and his men access.
At a conclave, the other Barons find the Widow guilty of violating the Foundation Treaty after her oil field attack, and decide to banish her from the Badlands. Quinn and his men surround the gathering and start attacking the Barons, who also turn on each other. While the subsequent battle takes place, Quinn catches Ryder and challenges Ryder to kill him. When Ryder hesitates, Quinn kills him instead.
After Ryder’s death, Jade claims the Baron position and forms an alliance with Lydia, who wants revenge against Quinn.
Quinn returns to his bunker and begins to hallucinate with visions of Ryder. Ryder’s apparition makes Quinn second guess if his tumor is gone. Quinn holds a knife to Henry’s throat, but Veil insists he’s healing and kisses Quinn to distract him.
Bajie takes Sunny to see his friend Nos, with whom Bajie plans to trade Moon’s sword for passage through a tunnel under the wall into the Badlands. While at Nos’s compound, Sunny learns of Quinn’s survival. One of Nos’s Dolls, Portia, fears for the future of Amelia, her daughter, and offers to pay Sunny to kill Nos. Sunny refuses, but later, he and Bajie fight Nos’s men and rescue Portia and Amelia. They all escape, with Moon’s sword, in one of Nos’s cars.
Lydia and the Armadillo Clippers attack Quinn’s bunker, but a bomb explodes. Veil uses the distraction as an opportunity to escape with Henry. Quinn captures Lydia.
Tilda opens up to Odessa about her traumatic childhood and how the Widow saved her from a life of sexual abuse by the Widow’s husband. Odessa and Tilda kiss.
M.K. escapes the Monastery. During his journey, he gets into a fight with a Nomad and learns his dark power no longer activates when he’s cut. Ava finds him and guesses the mirror chamber affected his gift. They continue running.
Veil flees to the Widow’s Sanctuary. The Widow offers to help find Sunny in exchange for Veil giving up Quinn’s location. The Widow also asks Veil to translate the hieroglyphic text in her Azra book.
Sunny and Bajie drive Portia and Amelia to a healer named Doc Cloud. Three Abbots use a tracker to locate M.K. and their device leads them to Doc Cloud’s apartment. Bajie hides while they search. Later, Bajie lets on about a connection he has to the Abbots but doesn’t give up any details. Sunny, frustrated by his secrets, drives off without him to find M.K.
The Widow invites Quinn to her Sanctuary to propose they work together to kill the other Barons. Quinn demands she first return Veil and Henry, but the Widow refuses. Later, the Widow finds that Veil is unable to translate the Azra book. She confronts Veil about having tried to get Tilda to poison her and can’t find a reason to forgive Veil. She turns her and Henry back over to Quinn.
M.K. and Ava rest at a lodge where M.K. finds an old magazine that features Azra’s skyline on its cover. The Abbots track them down. Sunny finds the lodge and reunites with M.K., and helps fight the Abbots. During the attack, Ava is killed while protecting M.K. Bajie arrives and helps take down one of the Abbots, Cyan, who he greets as “brother.” Bajie admits he used to be an Abbot. Cyan attacks Sunny with the Hand of Five Poisons, a deadly technique, before Sunny slices Cyan’s face in half.
Jade’s Cogs turn on her after the Widow attacks Jade’s mansion. The Widow expects Quinn to kill Jade, but he has her taken to the border and left on her own instead.
After Cyan’s attack, Sunny falls into a coma, and is sent into a dream-state where he imagines living with Veil and a 10-year-old Henry at a farmhouse. In his dream, a ghostly girl named Artemis haunts him and ominously threatens his family.
In the present, Sunny’s organs start failing. M.K. suggests sneaking into Master’s chamber at the Monastery to find a cure. Bajie hesitates, but M.K. mentions Sunny’s compass and his plan to get to Azra and Bajie agrees. On the road, Bajie tells M.K. about his history at the Monastery and training a Novice named Flea. Bajie says Flea was cleansed, but he brought her back using his own gift, which is why he doesn’t have it anymore.
Once they make it to the Monastery, M.K. steals the cleansing needles. Bajie secretly pockets the compass M.K. mentioned but doesn’t tell M.K. Before they can escape, the Master appears. A fight breaks out between Bajie, M.K., the Master, Novices and Abbots. Bajie and M.K. manage to escape.
In Sunny’s dream life, Henry kills Veil and longs to be a killer. Artemis reveals herself as someone Sunny once killed. Sunny is plagued by the ghosts of all the lives he took.
In the present, Bajie uses the Master’s needles to save Sunny and wake him from the dream. Bajie, Sunny and M.K. continue to the Badlands.
The Widow kills Baron Hassan and presents his head to Quinn. Quinn presents Baron Broadmore’s head in return, along with those of Broadmore’s innocent wives and children. Though killing Broadmore’s family is against what the Widow believes, she continues the alliance.
Bajie offers Nos’s car to a smuggler in exchange for passage through the wall surrounding the Badlands. Baron Chau’s Clippers catch Bajie, M.K. and Sunny and they’re brought back to Chau’s Cog pens.
Chau learns of Sunny’s Clipper past and offers him a position as Regent in order to get rid of the Widow. Sunny plans to use M.K. to lure the Widow into the open, take her down and be led to Quinn. Bajie assumes he’s being left behind as a captive, but Sunny slips him a metal bookmark so he can pick the lock of his cell. When the coast is clear, Bajie breaks out and steals a motorcycle to follow Sunny and M.K. Sunny assures M.K. he’s only pretending to trade him.
One of Chau’s Clippers lures the Widow by telling her Chau is trading M.K. to the River King. At the bogus sale, the Widow realizes she’s been set up once Sunny appears. The Widow tells Sunny she knows where Veil and Henry are. Sunny cuts down Chau’s Clippers and stands with the Widow. The Widow vows to work with Sunny to kill Quinn.
Quinn marries Veil against her wishes.
Sunny and M.K. arrive at the Widow’s Sanctuary, where the Widow learns M.K. no longer has his power. Bajie pretends to be a hurt Cog and is allowed into the Sanctuary.
M.K. offers Tilda to come with him to find Azra, but she declines and mentions her growing relationship with Odessa. Later, Odessa tells Tilda she was a part of the Cog shipment where M.K. slaughtered people and warns Tilda to stay away from him.
After Quinn learns of Sunny’s ambush and new alliance with the Widow, Gabriel arrives at the Widow’s Sanctuary with a bomb secretly strapped to his chest. He warns Sunny that the Widow is the one who traded Veil to Quinn, then blows himself up. Sunny runs off to pursue Quinn alone.
Bajie finds M.K., comes clean about stealing the compass and attempts to steal the Azra book. The Widow stops them and admonishes Bajie for abandoning her at the Monastery. M.K. realizes Bajie’s Novice, Flea, is the Widow.
Tilda confronts the Widow about how power has shifted her morals and regrets not poisoning her. The snide remark prompts a vicious and bloody fight between them, with the Widow knocking Tilda unconscious.
Lydia sees bundles of explosives fastened to Quinn’s bunker walls and realizes he’s ready to kill everyone before he lets Sunny take Henry. Lydia warns Quinn’s men but realizes they’re all willing to die for him. Quinn sentences her to death for trying to corrupt his men.
The Widow plans to use the Azra book to get both her and M.K.’s gifts back. She orders Bajie to translate the Azra book to determine how.
Two Loyalists guard Lydia as she digs her grave. Lydia uses the shovel to kill one. The other chases her through the woods until Sunny appears and kills him. Lydia warns Sunny that Quinn has rigged the entire bunker to explode, but Sunny continues on.
Tilda wakes up in a cell after her fight with the Widow. Bajie, locked away next to her, introduces himself as M.K.’s friend. Odessa appears and frees Tilda, but admits she’s the one that turned M.K. and Bajie in. Tilda has Odessa free Bajie as well so he can save M.K.
Tilda and Odessa steal a car to flee the Sanctuary. Tilda invites Waldo, but he declines, not revealing that the Widow has offered him a Baron position.
Sunny arrives at Quinn’s bunker. Quinn launches an arrow at an explosive wired to the roof and Sunny’s left buried underneath the debris.
Bajie makes it to Quinn’s bunker and frees Sunny from the rubble. They take out Quinn’s Loyalists together. Sunny finds Veil while Bajie stays behind to take out one remaining Loyalist. Bajie kills the Loyalist, but ends up wounded after a pair of scissors are jammed into his gut. He remains determined to “save the world.”
Sunny finds Quinn and they face off in an epic showdown. Sunny finally plunges Moon’s ringed sword into Quinn’s gut, but before he can escape with Veil, Quinn grabs Veil from behind and offers her in exchange for Henry. Veil sacrifices herself by plunging Quinn’s sai into her own throat and impaling Quinn in the process. Sunny buries Veil and sets off into the woods with Henry in his arms.
Bajie rides on Sunny’s motorcycle to an ancient stone citadel on the edge of a cliff with rusted satellite dishes on top. Inside, he finds a control room and opens the Azra book to a page full of symbols matching those on a console’s dials. The compass inside the book spins and point towards the written symbols. Bajie adjusts the corresponding dials until the console beeps and comes to life. “Azra,” he whispers.