Off the coast of Lagos, Nigeria, an ancient swordfish rams an offshore oil-loading hose to stop the pollution fouling her ocean. A tremendous sound erupts from the water, and a glowing mass settles on the ocean floor, drawing sea creatures with clean water. Those that approach are physically transformed: The swordfish triples in size, gaining golden, impenetrable skin. The ocean now teems with aliens and monsters.
On Bar Beach at 11:55 p.m. on January 8, 2010, three strangers converge, each fleeing a personal crisis. Adaora is a marine biologist at the University of Lagos whose husband, Chris, a wealthy accountant turned born-again Christian, has slapped her for the first time in their ten-year marriage. Anthony Dey Craze is a famous Ghanaian rapper who left his concert after hearing strange music and seeing visions of trees among his audience. Private Agu, a member of Nigeria's Igbo ethnic group, was beaten by fellow soldiers after stopping his superior, Lance Corporal Benson, from raping a woman at a checkpoint; Agu punched Benson with superhuman force. The three barely begin speaking before a deafening boom knocks them flat, and a massive wave drags all three into the sea.
When Adaora awakens on the beach, a strange woman stands over her, saying her people have landed in the water and want help. Adaora names her Ayodele. The name is Yoruba, from another of Nigeria's major ethnic groups, and Adaora chooses it partly because Chris would distrust a Yoruba stranger in his Igbo household. Adaora brings Ayodele, Agu, and Anthony home. Under her microscope, she discovers the alien is composed of tiny metallic balls rather than biological cells, explaining her shape-shifting.
Chris storms downstairs, enraged to find strangers in his home. Ayodele shape-shifts into an exact copy of him, producing a sickening alien sound. Chris flees, screaming that Adaora is a "marine witch," and drives to Father Oke, his manipulative bishop, who confirms his suspicions. The next morning, Father Oke tries to recruit Ayodele, envisioning her shape-shifting as a tool to grow his church. Philomena, the family's house girl, secretly records Ayodele's transformation.
Adaora films a video in which Ayodele declares herself an alien ambassador, stating her people chose Lagos and intend to stay. Ayodele reveals a plan: Anthony will use his celebrity to draw a crowd, Agu will approach Benson, the president's nephew, to reach the president, and Adaora will serve as scientific expert. Philomena shows the footage to her boyfriend Moziz, a 419 scammer (a practitioner of Nigerian advance-fee fraud), who plans to kidnap the alien.
Anthony's manager spreads word of a free concert, drawing hundreds to Adaora's house. Adaora's eight-year-old daughter, Kola, begins filming Ayodele and the crowd. Father Oke's congregation and the Black Nexus, an underground LGBT student organization, also converge on the house. Moziz and his crew burst in with guns, but Ayodele transforms into a lizard and escapes outside. On the lawn, she shifts back to human form and addresses the crowd, asking what they will do with the change her people bring. Her speech broadcasts on every screen in Lagos, whether turned on or not.
Agu and Adaora's attempt to reach the president through Benson goes badly. En route, they share a brief, impulsive kiss. Benson dismisses the alien story, has soldiers beat and arrest Agu, and forces Adaora to lead him to Ayodele. At the house, Benson orders soldiers to shoot Ayodele. They fire, hitting her and also striking Kola in the arm. Ayodele retaliates: The soldiers explode, and she rearranges their remains into a plantain tree. She heals Kola by sending part of herself into the child's arm. A second sonic boom plunges the city into chaos. Area Boys (gangs of street youths) loot and burn, and citizens attack suspected aliens.
Agu, taken to sea on a military speedboat, survives a monster attack and is carried to shore by a sentient manatee. He watches hundreds of alien beings walk out of the ocean as an enormous ship rises on the horizon. Ayodele retreats into a tiny monkey form, refusing to speak. Adaora discovers she can levitate, confirming latent supernatural abilities. Chris, who saw the kiss, confronts her; Adaora convinces him to take the children to safety.
Across Lagos, the night of chaos transforms the city. Moziz shoots his friend Jacobs upon discovering Jacobs's cross-dressing, and an alien kills Moziz in retaliation. Father Oke's followers attack the house with Molotov cocktails, and Anthony unleashes "the rhythm," a sonic power he discovered at age ten, knocking everyone in a three-mile radius unconscious and extinguishing the fires. On the drive to the airport, the group encounters Fisayo, an unhinged woman who also witnessed the original wave. Fisayo shoots and kills a boy who cannot speak; Ayodele disperses Fisayo at a molecular level. The boy's death, captured on camera, becomes iconic.
At the Lagos airport around 6 a.m., the group intercepts the president's plane. He emerges weak after heart surgery in Saudi Arabia. Ayodele proves herself by shape-shifting into Karl Marx, his secret ideological hero, then heals him. He emerges sharp-minded and asks to meet the alien Elders.
The boat journey is harrowing. Monstrous sea creatures attack repeatedly. Adaora discovers she can walk on water and project a force field; Agu hurls a giant shark into the air; Anthony unleashes the rhythm underwater. Beneath the ocean, Adaora's legs fuse into a fish tail and she develops gills. Born with webbed hands and fused legs that were surgically separated in infancy, she has become the mermaid her body always suggested she could be. The president meets with five alien Elders, who inform him all offshore drilling will end but offer their technology in exchange.
When the group returns to shore, traumatized soldiers beat Ayodele savagely. She does not fight back. Adaora pushes the soldiers away with her force field and cradles Ayodele. Ayodele says her people sent her knowing this would happen: "Your people need help on the outside but also within. I will go within." She releases a final sonic boom and dissolves into a white mist that rolls over Lagos. Ayodele has seeded change within every Lagosian.
The president delivers a televised address on every screen in Nigeria, naming Adaora as scientific expert, Anthony as celebrity ambassador, and Agu as security lead. He declares corruption dead and urges citizens to call their neighbors "brother." Chris takes in an alien; his mother later welcomes nine more. Father Oke encounters Mami Wata, the water goddess, follows her to the beach, and is never seen again.
Adaora watches three women absorb the president's speech on their phones, then look at each other and laugh. She whispers, "I am a marine witch," reframing her husband's insult as an identity rooted in her power. Udide Okwanka, the Great Spider who narrates the novel from her cave beneath Lagos, reveals a final threat: Other nations are considering a nuclear strike on the city. For the first time, Udide declares she will leave her web and join the fight. In a postchapter, three African-American college students in Chicago debate whether the footage is real, then return to studying, an ironic coda on the world watching Africa's transformation with detached curiosity.