The book opens with a scene of Nicol Bolas in his lair on Grixis, getting snappy with some of his minions (including the demon-dragon Hybrid Monster Malfegor) while brooding over his plan to collide the five shards and harvest the mana from the resulting kaboom to restore his power, which had been drained by the events of Future Sight.
Then we have a lot of things happening all at once.
Cut to Ajani Goldmane in Naya, just after the events of Part 1 of Flight Of The White Cat. He's out hunting a massive gargantuan. Some brief exposition reveals that he's been rejected by his peers because of his rare albino fur, but his brother Jazal (the pride's leader, or kha) has always protected him. Anyway, he's fighting the giant monster. He manages to kill it, but unfortunately, he's found by his Jerk Jock pridemate Tenoch and his gang of hangers-on. Tenoch beats up Ajani and takes the credit for the kill. Ajani gets back to camp and is comforted by his childhood friend Zaliki before the pride's big feast, where a storyteller recounts the legend of Marisi, the nacatl hero. Ajani notices that Zaliki looks worried, but she rebuffs him. That night, the camp is attacked by mysterious hooded nacatls, and Jazal is murdered. Ajani discovers Zaliki with the body and, in his grief, his planeswalker spark ignites and he wakes up on Jund.
Meanwhile on Bant, we meet Gwafa Hazid, smuggling some illicit goods in his caravan. As some knights approach to inspect the wagons, he gives one of his men a dagger and suggests in a whisper to do something useful with it. Said henchman starts sneaking up on one of the knights, and the cunning Gwafa Hazid shouts a warning; the knight kills the knife guy. But this isn't enough to distract the knight, so Gwafa stabs him himself and moves along. His caravan approaches Giltspire Castle. He sends his mages out to perform a ritual while he meets with some customs agents. His fast talk doesn't convince them, and they try to stop the caravan, so Gwafa has his wagons make a break for it. They make a circle around the castle and the mages finish a ritual that causes the castle to crumble; only a bright white obelisk remains. Gwafa is astonished and chagrined—he didn't expect that to happen, and thinks, My God, What Have I Done?
On Jund, we meet Rakka Mar, another of Bolas's minions. She's out preaching to a warrior tribe (led by Kresh the Bloodbraided), riling them up to go hunt a local dragon named Malactoth. After she's done, Kresh follows up with a Dare to Be Badass speech, egging them on further. Then they lead an expedition to the dragon's lair, but they're ambushed by some viashino. There's a skirmish. Rakka Mar insists that they continue onward despite losing eight of their men. As they approach Malactoth's volcano, they encounter Sarkhan Vol going to meet the dragon as well; he joins their party, expecting the dragon to eat them all anyway. They charge at the dragon (and Sarkhan uses his +1 ability to give them +1/+1 and haste until end of turn), but the battle goes poorly, and Sarkhan is forced to cast Form of the Dragon. As the Scaled Up Sarkhan battles the hellkite, Rakka reveals that the whole thing was a diversion so that she could raise another obelisk. Kresh and Sarkhan finish off the hellkite as the cave collapses, and Sarkhan leaves to investigate the purpose of the obelisk. Instead, he finds Ajani, who's just dropped out of the sky and onto the plane of Jund.
On Bant again, we meet Rafiq of the Many, who's preparing for a combat. His friend and second, a rhox knight named Mugin, tells him that he'll be inspected by a group of aristocrats from the Order of the Skyward Eye. As Rafiq enters the arena, he notices that his opponents' swords are unusually sharp. Rafiq and Mubin easily win the first match, but in the second round, Rafiq is astonished when his opponents start performing illegal maneuvers: they aim for his head, slash at his armor, and attack him from behind, drawing blood. As Rafiq realizes that they're fighting to kill, they take off their armor, knowing that the honorable Rafiq of the Many would never fight and injure an undefended enemy. Rafiq, ashamed, fights them anyway and wins. After the fight, the inspector congratulates him on showing the ability to fight under the atypical conditions, and sends him on a mission to discover how Giltspire Castle was destroyed. Rafiq investigates the ruins and encounters Gwafa Hazid's trail. Gwafa is still shaken by what he's done when Rafiq catches up to him and places him under arrest.
Back on Jund, Sarkhan chases away a dragon that's about to attack Ajani, and introductions ensue. Sarkhan explains that Ajani is a planeswalker, and brings him to a caldera to show him the power of red mana. Ajani jumps into the volcano, embracing his anger. When he wakes up, he's in Naya again, and he vows to kill everyone responsible for his brother's death. He starts to have hallucinations of his brother talking to him as he returns to his camp in the wake of Jazal's funeral. After speaking with Zaliki, who tries to calm him down, he storms into the forest to look for Tenoch, his first suspect. When he finds Tenoch, he partakes in some High-Altitude Interrogation, but it backfires, and in the struggle he falls off the cliff himself.
Elsewhere on Naya, we find Nicol Bolas conversing with Marisi, who, it turns out, is very much alive, and working for Bolas. Marisi has been charged with stirring up conflict. He informs Nicol Bolas that the elves rely on the guidance of the mythical world-hydra Progenitus; they believe their shaman, Mayael, can converse with it directly.
Back on Jund, Sarkhan finds and confronts Rakka Mar. She leads him to Nicol Bolas. Sarkhan is in awe and cows in the presence of the most magnificent dragon he's ever seen. He swears fealty to Bolas and tells him about Ajani.
Meanwhile on Bant, we meet Elspeth Tirel, a planeswalker with no desire to planeswalk. She's happy as a knight of Bant and conceals her abilities from the other Bantians. She's shocked when a wounded Ajani Goldmane appears out of thin air on a nearby hill, but she brings him back to the healers and encourages him to stay on Bant, which she considers a paradise. However, Ajani insists on leaving to seek his revenge and returns to Naya. Before he goes, he warns Elspeth about the coming Conflux.
On Esper, the Seekers of Carmot, under orders from Nicol Bolas delivered via Sarkhan, confront a lighthouse operator and force him to act as a Telemin. The mind-controlled lighthouse operator dives into the ocean and activates the Obelisk of Esper.
Ajani, after teaching himself to cast Lightning Helix on an elemental guard, interrogates Tenoch's mother and discovers that she's been in contact with Marisi. He tracks down Marisi, who has been busy at the Relic of Progenitus performing a ritual for Bolas. When threatened, Marisi spills his guts about Nicol Bolas's plan to smash the shards together and devour the plane's energy, revealing that Jazal was killed for inadvertently getting in the way of Bolas's plans by trying to forge a peaceful alliance with another nacatl faction. A sudden earthquake allows Marisi to escape just as a party of elves, led by Mayael, arrives at the Relic. Ajani notices a spell vessel that Marisi left behind and cautions the elves to beware. He leaves to look for Bolas.
Mayael attempts to commune with Progenitus, but unbeknownst to her, Marisi's spell has allowed Bolas to hijack her connection to the world hydra. Bolas tricks her into going to war with the other shards.
At this point, the Conflux happens and the five shards start to collide.
At the very center of the convergence, The Maelstrom forms. A smug Bolas observes the collision, knowing that the obelisks will funnel mana into the Maelstrom for him to harvest.
We get some brief glimpse of how some of the human refugees from Grixis are holding up. Oh, and the events of the Honor Bound webcomic correspond roughly to this point in the novel, but that's offscreen.
On Bant, a council of war is held. Rafiq is chosen to lead Bant's forces against the invaders from Esper and Grixis. He and Mubin and their army (including Elspeth) go to meet the forces from Esper. However, accustomed to the honorable Combat by Champion of Bantian warfare, they're unprepared to fight against Esper's magics, and suffer severe casualties. Elspeth, desperate, gives one of her soldiers +3/+3 and flying until end of turn to attack an airborne Esper mage. Mubin is hit by a mind-control spell and attacks Elspeth, and Rafiq is forced to fight his best friend. Both Elspeth and Mubin awake later in a hospital. Mubin's spine was damaged, and he's paralyzed from the waist down.
Bolas congratulates Sarkhan on a job well-done, granting him five mind-wiped dragon servants for him to control. Sarkhan is conflicted at seeing majestic dragons cowed and defiled by Bolas's magic, and recognizes Karrthus among the five. He accepts the gift nevertheless and flies off to attack Naya. Afterwards, Bolas confers with Malfegor, sending him to attack Bant and finish the job Gwafa Hazid started before being captured.
Ajani returns to Jund and meets Kresh. Kresh and his tribe welcome Ajani as a spirit to guide them; Ajani asks about Bolas. Kresh happily goes with Ajani to find Rakka Mar. They chase her to the Grixis frontier, but she refuses to help them.
Rafiq leads an invasion force to Esper and captures a mage, questioning her about the secrets of etherium. Meanwhile, Elspeth visits Gwafa Hazid in his cell and interrogates him, learning about Bolas's involvement. Mubin makes an important discovery about the Prayer of Asha, the prophecy that advised Bant to go to war, and forces himself out of bed and into a caravan.
Mayael assembles an army of gargantuans as Sarkhan's dragon army invades Naya. They fight. Bant's forces reach Grixis, discover the refugees from a few chapters ago, and rescue them. The refugees warn them about Malfegor's forces approaching the Bant frontier, and Rafiq decides to intercept them. Their forces meet at Giltspire and Malfegor finishes activating the Obelisk of Bant. At the last minute, a messenger arrives, carrying the lost Sword of Asha, which Mubin discovered in the gardens of Valeron. Rafiq wields the sword, and after Elspeth casts her Angelic Blessing spell on him, he's able to slay Malfegor (in two strokes, of course) and Bant stands victorious.
Marisi reveals himself to the Wild Nacatl tribes and unites them to attack the Cloud Nacatl as part of a plan to activate the Nayan obelisk, but Zaliki confronts him, and we learn that she was the one who betrayed Jazal. She realizes she's been duped and attacks Marisi, but it's too late—he's already activated the final obelisk.
Meanwhile, energy is being secretly funneled from all the spells being cast in the wars through the obelisks, feeding the Maelstrom. Ajani arrives at the Maelstrom with Kresh's tribe at the same time as Mayael's army. Zaliki is with them; she tearfully confesses to Ajani that she was the one who killed Jazal. Ajani is shocked, but as he refocuses his rage towards Bolas, Sarkhan appears, and the forces clash. Ajani sees their magic feeding the Maelstrom and uses his ultimate ability to sever all of the mana ties, cutting the vortex off of its energy supply just as Nicol Bolas himself appears.
Bolas swats Ajani aside easily and starts absorbing the Maelstrom's energy, but Ajani dives into it and absorbs some of the energy for himself. Infused with this extra mana, he uses his other ultimate ability to summon an Avatar of Nicol Bolas. The two dragons fight. Confronted with the only power that can match his own—himself—Bolas retreats without devouring the rest of the plane.
In the final scenes, Elspeth leaves Bant sadly, no longer the innocent paradise it once was. Rafiq's attempt to heal Mubin's legs with etherium infusions fails, and Mubin dies. Ajani makes his peace with Zaliki and leaves Alara to roam the multiverse.