The Rosewater Redemption is the third volume in the Wormwood trilogy by Nigerian-British author Tade Thompson. It concludes a major new work of science fiction, one that mixes and matches familiar tropes with an unfamiliar setting, and in so doing changes their significance.

The first volume, Rosewater, won the Arthur C Clarke award earlier this year and is set in a mid-2060s Nigeria. Fifty years earlier, a gigantic alien lifeform dubbed Wormwood crashed into London and sank into the ground. Moving through the Earth’s crust, Wormwood re-emerged in Nigeria, where it unleashed alien animals and bacteria, but also began healing illness and injury. The city that sprang up around this healing spring called itself Rosewater.

The alien bacteria released into the atmosphere by Wormwood form the “xenosphere”, which connects all living beings on the planet. Some humans, like Rosewater’s protagonist Kaaro, are able to sense the xenosphere and manipulate it, giving them psychic powers. At the end of that book, Kaaro and his lover Aminat, who are both agents of the secret government department S45, discover that Wormwood, by performing healings and seeding the xenosphere, is transforming human cells into alien ones, slowly remaking the human race.

Rosewater was a meditative novel, dominated by Kaaro’s cynical worldview and ambivalent about the prospect of alien transformation. The later volumes have shifted tone towards the adventurous; Kaaro becomes a secondary character while the more dynamic, heroic Aminat takes centre stage. In The Rosewater Insurrection, published earlier this year, the purpose of Wormwood’s actions is revealed to be the conversion of humans into suitable receptacles for the stored memories of Wormwood’s alien masters, whose own planet was lost to ecological catastrophe.

Aminat and Kaaro’s former boss at S45, Femi Alaagomeji, is determined to prevent this takeover, to which end she exploits the political tensions between Rosewater and the Nigerian government. Jack Jacques, the charismatic but monomaniacal mayor, declares the city’s independence just as the first alien personality transfer takes over the body of a middle-class woman, Alyssa Sutcliffe, who eventually becomes Wormwood’s avatar.

At the end of that novel, the Rosewater leadership and the aliens reach a detente, but as The Rosewater Redemption opens, those relations are already breaking down. As alien separatists attack humans and the Nigerian government bankrolls a gang war within the city, Aminat, now Rosewater’s head of security, must decide whether to remain loyal to the mayor and his vision of an independent city, or join Kaaro in assisting Femi’s plot to get rid of the aliens once and for all.

As he did in the previous volumes, Thompson constructs a vivid, almost overwhelmingly detailed future world, which combines the biological and the technological, human and alien. The xenosphere functions as a sort of spore-based cyberspace, where adepts like Kaaro exist alongside traditional hackers, who combine disciplines with him in search of a weapon to use against the aliens. In the physical world, alien animals – “floaters” who consume human flesh; giant worms that burrow into the ground and emerge to topple buildings – fight for resources and living areas with animal-form robots and surveillance drones. The very definition of personhood is challenged by beings such as the revolutionary Oyin Da, a ghost who exists solely in the xenosphere, or Lora Asiko, a sex robot converted into an assistant by the mayor who has control over her own programming.

Given this theme of cross-pollination, one might expect the Wormwood trilogy to hold out the possibility of coexistence. But while stories of alien invasion are common in science fiction, they are rarely told from the perspective of the formerly colonised. Some humans, like the mayor, believe the benefits the aliens offer are worth the eventual takeover they intend; others, like Femi, look to their nation’s past for a lesson in the foolishness of hoping for the best from colonisers. The countries of the west, meanwhile, are refreshingly absent from this story, with the US quarantining itself off on realising the aliens’ intentions, leaving the fate of humanity in the hands of the Nigerian heroes.

With the previous novels’ introduction of cellular-level transformation still fresh in the mind, readers might question whether the characters’ goal of rolling back the influence of alien colonisers is even possible. But The Rosewater Redemption is a stunning conclusion to a trilogy that expands our understanding of what science fiction can do.

• The Rosewater Redemption by Tade Thompson is published by Little, Brown (RRP £8.99). To order a copy go to guardianbookshop.com or call 020-3176 3837. Free UK p&p over £10, online orders only. Phone orders min p&p of £1.99.