Onyx Storm opens in the immediate aftermath of the previous book in the series, Iron Flame. The kingdoms of Navarre and Poromiel, along with the leaders of the revolution, are negotiating an alliance to defeat the venin army—a fleet of dangerous dark wielders that have been wreaking havoc just outside Navarre’s borders. The meetings are not going well, however, and Violet realizes she must take matters into her own hands to save the peace negotiations. Violet is also committed to finding the cure for venin so she can save Xaden, who started to turn venin at the end of the previous book.

A group of venin infiltrate Basgiath in an attempt to rescue fellow venin Jack Barlowe, who is being kept in the Basgiath dungeon. Violet and her friends manage to kill several, but in the midst of the conflict Violet notices that one of the venin has silver hair like her. Violet is later summoned to a meeting with the Senarium, the council of nobles who represent each of Navarre’s provinces, where she pitches a quest to find the rest of Andarna’s kind, the elusive seventh dragon breed. Violet believes they are the key to defeating venin. Her quest is approved, but she is outraged to learn that Professor Grady will lead the expedition instead of her. Xaden soon returns from his own meeting and tells Violet he has been reinstated as the Duke of Tyrrendor. 

The peace negotiations are nowhere close to being resolved, so Violet decides to commit treason by altering the Basgiath wardstone so that gryphon fliers will be able to wield their signets within the wards. Violet cleverly avoids being punished, and Poromiel finally agrees to the alliance now that the fliers can use their powers. General Aetos, Dain’s father and the new Commander of Basgiath War College, is furious that Violet has escaped punishment and sends her and her squad to serve active duty at a Navarre military outpost for a few days. While there, they learn that Newhall, a nearby village, is being overrun by venin, and they decide to help rescue civilians. 

When Violet and Tairn arrive in Newhall, they find themselves caught in a tornado. Tairn is knocked unconscious, and Violet is soon set upon by a silver-haired maven (a high-ranking venin) named Theophanie. Theophanie can wield lightning, and she wants Violet to turn venin with Theophanie as her mentor. She also expresses an interest in Andarna. Theophanie surprises Violet by letting her go, and she returns to Basgiath with the rest of her squad. Xaden admits he nearly lost control and channeled when he realized Violet was in danger, and Violet is committed more than ever to finding a cure for the man she loves. 

Xaden is sent to the front, worrying Violet; beyond the wards, it will be easier for him to slip. She interrogates Jack about the cure for venin, but this proves unhelpful, as Jack claims there is no cure because no venin wants to be cured. Violet and her friends continue to research both venin and the mysterious seventh dragon breed. She eventually has a breakthrough and realizes her father’s final research project might contain useful information, and she enlists Dain to help her steal it. Once it’s in her possession, she finds a letter instructing her to go to Deverelli. Halden, Navarre’s crown prince and Violet’s ex-boyfriend, also arrives and delivers a message from Viscount Tecarus, who has arranged a meeting with King Courtlyn of Deverelli in exchange for an artifact that is trapped in the venin-infested city of Anca. 

Violet, Xaden, Mira and a few others selected by Professor Grady head to Anca. They manage to retrieve the artifact but the group’s incompetence leads to two deaths. As a result, Violet successfully demands that she obtain full control of future missions to find allies and the seventh dragon breed (also known as “irids”). The new squad consists of Violet, Xaden, Ridoc, Dain, Mira, Cat, Maren, Trager, and Drake (Cat’s cousin). Unfortunately for Violet, the squad also has to include Halden and his guard, because many territories will require an audience with a representative of Navarre’s royal family. 

The squad lands in Deverelli and Xaden finds relief for the first time in weeks because it is a land without magic. The lack of magic also cuts everyone (except for Violet) off from their dragons, and none of them can wield. Halden meets with King Courtlyn and Violet takes the remaining squad members to retrieve the rest of her father's research. They soon learn that Halden is being detained by the king, and Xaden and Violet head to the palace to get him back. King Courtlyn sends guards to kill Violet, Xaden, and Halden, causing Xaden to lose control and channel. Violet, with the help of Andarna, manages to negotiate their release and conceal the true nature of Xaden’s outburst. The group returns to Basgiath, and Violet is dismayed to see that the gold flecks in Xaden’s eyes have turned amber—an indicator that his venin abilities are growing stronger. The quest squad prepares to search the next isle and Aaric reveals his secret identity as King Tauri’s youngest son, enabling him to replace the incompetent Halden during their next mission. 

Their first stop is the Isle of Dunne, where Xaden, Dain, and Violet are selected to fight for an audience with the queen, but there are no irids on the island. Violet is approached by a silver-haired priestess of Dunne who implies that Violet was almost dedicated to the goddess as a child. Their next stop is Hedotis, the Isle of Wisdom, and Xaden is horrified to discover that his mother (who abandoned him when he was ten) is married to a member of the isle’s triumvirate—that is, the three people who govern Hedotis. The triumvirate tests the squad but Violet outthinks them and secures an alliance. Their third stop is Zellyhna, an island dedicated to the god of luck. The mistress of festivities demands that each member of the quest squad accept a gift chosen by fate, ultimately leading to Trager’s death when he is “gifted” an arrow to the heart.

Quest squad travels to a smaller isle nearby to burn his and his gryphon's bodies. A group of irids emerge and speak to Violet, though they are not bonded. The irids ask Andarna to tell her story, and when she is done they say that she is proof that humanity has failed; she has, as they feared, been turned into a weapon. They refuse to help in the upcoming war and tell the group there is no cure for venin. Ridoc realizes that Xaden is venin, and demands Violet tell the rest of their friends when they get back. 

Quest squad dejectedly returns to Basgiath empty-handed. Xaden starts to distance himself from Violet, likely reeling from the irids’ characterization of him as an “abomination,” and Violet worries he has given up on finding a cure. Things take a turn for the worse when Lynx, one of the first-years in Violet’s wing, manifests as a shadow wielder, proving that magic has rejected Xaden as their generation’s only shadow wielder. 

Violet and her squad head for Aretia for a two-week rune intensive. She is disappointed that Xaden is not home, but is pleased to hear that Xaden and Brennan have been working on a cure—proof after all that Xaden has not fully abandoned hope. During Violet’s stay in Aretia, Xaden returns and the two of them have sex for the first time in weeks, due to Xaden believing he has learned how to control the urge to channel. That night, Violet and Xaden have the same dream and they realize Violet’s second signet has manifested—she is a type of inntinsic known as a “dream-walker.” The couple barely has time to process this discovery when Tairn warns Violet that venin are heading their way. Aaric tells Violet she needs to defend the temple of Dunne to save Tyrrendor and she does, protecting the priestesses and the temple from Theophanie. During the battle, Violet realizes Theophanie was a high priestess of Dunne before she turned venin. Leothan, one of the irids, arrives at the last minute and fires Aretia’s wardstone, causing the venin to retreat. He then asks Andarna to break her bond with Violet so she can go with him to learn the irid ways. Andarna is torn, but ultimately chooses to do so.

Andarna’s departure causes Violet to sink into a depression for several days. On the fourth day, Mira arrives, and Violet learns her father tried to dedicate her to Dunne as a baby because of her sickly nature. However, the priestess would not accept her because her fate was uncertain. During the argument that ensues, Xaden reveals he is venin and Mira storms off, offended that people have been keeping secrets from her again. Later, an injured Garrick returns from patrol with a message from Theophanie: the venin have taken Draithus, and Xaden must bring Violet and Jack to meet her there or she will kill Mira. The Assembly decides that Violet will attempt to take out Theophanie while the rest of the riders and fliers defend Draithus. 

Violet and Xaden use Jack to bargain for Mira’s life, but Theophanie slits Mira’s throat and disappears. Brennan tries to mend her—but the damage is too great. Dain and Sloane arrive at the last minute and Sloane uses her siphoning signet to transfer some of Dain’s power to Brennan, allowing him to save Mira. Sloane also gives Violet a package from Aaric. Xaden and the others leave to defend the city while Violet waits for Theophanie to return.

Theophanie arrives and Violet realizes Theophanie is a storm wielder, not a lightning wielder. Violet and Theophanie fight while the venin wreak havoc on the city. The point of view briefly shifts away from Violet to Rhiannon and Imogen as they fight the venin-controlled wyvern. Many are injured and Quinn, Imogen’s best friend, is killed in the fight. 

Theophanie and her wyvern fly away, and Violet and Tairn give chase. A net is dropped on Violet and Tairn and they are nearly killed as they plummet to the ground. Violet loses her dagger in the fall, but notices that Aaric sent her a marble dagger from the high priestess of Dunne with a note instructing her to use it after she loses hers and to strike in the dark. Violet realizes Aaric’s signet gives him the ability to read the future. The city becomes shrouded in shadows and Violet realizes that Xaden is channeling to save them all. She uses their bond to tell Xaden that she loves him and then kills Theophanie with the help of Andarna, who has returned, before collapsing. 

The next chapter is told from Xaden’s point of view. He chooses to sacrifice his soul to save Violet and Sgaeyl. However, he hears Violet’s whispered “I love you” and manages to stop before he loses himself completely. He is horrified to discover that someone close to him has also turned venin, but he does not reveal the identity of his new “brother.” He forms a plan with Sgaeyl but is only willing to go through with it if Violet agrees.  

Twelve hours later, Violet wakes up in Aretia with no memory after her killing of Theophanie. She learns that Xaden is missing, along with a few riders (including Garrick) and six dragon eggs. She is also married to Xaden, though she has no memory of having done so. When she asks Imogen why she wiped her memories, Imogen says that Violet asked her to.