From the opening page of this collaboration between the photographer Marc Atkins and the writer Iain Sinclair, we are led into a peculiar world of ghostly espionage. The first photograph sets out the themes and the take: an anonymous room full of shadows, empty apart from a video camera on a tripod, pointing through a shrouded window. It's an imaginary stake-out, an expression of Atkins's view of his own work, quoted in Sinclair's introduction: "All I can do is suggest scenarios."

The message one infers is: while a long lens does not guarantee reality, operating undercover - sneaking up on a subject - may be the only way to access a different kind of truth. So what's the target of this surveillance operation? Hidden beyond the curtain is the shifting city outside, but what of the surveillants themselves? Long gone.

Atkins and Sinclair have worked together before, most recently on the widely praised Lights Out for the Territory. While the raw material is similar - long journeys on foot across London's eastern and south-eastern quadrants - the snapper has a better gig here, higher billing in the advance publicity.

The 180 images in Liquid City demonstrate the ambitious scope of Atkins's vision. From high on the roof of a mock-Byzantine temple we look down on the Thames, its brilliant sheen offset by a shadowy high-rise skyline - a modern monochrome Canaletto, huge but depopulated, empty of all human activity.

Atkins captures forgotten places passed by en route to somewhere else - desolate post-industrial sites on the edge of the river, a static caravan flying a Union flag somewhere on the estuary, the Dartford river crossing rising triumphantly into the haze. He revels in derelict back-streets and decaying monuments - the cracked surface of the John Bunyan effigy in Bunhill fields, or his own shadow falling across William Blake's gravestone.

Alongside photographs of Michael Moorcock and Peter Ackroyd in the back of a cab or relaxing next to a street sign reading Dan Leno Walk SW6, Atkins portrays a litany of vanished writers. Some are dead (Kathy Acker, Derek Raymond), others are missing (David Gascoyne, a "natural psychogeographer" whose only novel explores Twickenham's "sublimely ordinary surfaces") and others are denizens of pubs too far from Clerkenwell for them to have tangled much with the mainstream media.

As for the images themselves, Sinclair is right when he says Atkins lacks the "tender human curiosity of Robert Frank" - the portraits feel cold, the remoteness of the subjects unpunctured. More haunting are his odd images, reminiscent of Man Ray's, of the human figure photographed in the intimacy of a curtained room. Atkins has worked the light over and over in the darkroom, burning away layers of detail, drawing down a veil that suggests roughed-up archive celluloid, transforming a person into an apparition.

Sinclair describes his collaboration with Atkins as one that never happened; rather it was "a series of accidents that occasionally fused discrete worlds". He tells us that they work in different directions. For Atkins the city is to be endlessly trawled in an attempt to return to a "state of disquiet". Driven to take photographs, Atkins has burdened himself with a huge archive of prints - a "displaced autobiography" - from which he cannot escape.

Of himself Sinclair says that the only autobiography he cares to deliver comes through exaggeration, seeing the city as a "theatre of possibilities in which I can audition lives that never happened". And he, too, cannot help himself.

Like a couple of spooks adrift behind enemy lines somewhere beyond the Isle of Dogs, Atkins and Sinclair travel incognito. The schoolgirls who decide they are suitable candidates for a questionnaire cannot know whom they are dealing with. Asked what he thinks of the Docklands transport system, Sinclair remembers being marooned on a DLR ghost train, "but that was in another country".

Liquid City is an impressive and bold act of dark necromancy. Sinclair conjures up the dead and those who have never lived as he moves between the past and the present, the real and the fictional.

And no one else could pose this question: "Where else but Charlton would you find a public toilet (closed for the duration) designed by Inigo Jones?" The city is in safe hands.

Tristan Quinn works for BBC2's "Newsnight"