In the summer of 2003, Grey began investigating reports of the CIA's secret system of extraordinary renditions (transfer of terror suspects to foreign jails, where many faced torture). The results of his research were first published in the New Statesman in an article headlined 'America's Gulag' in May, 2004.. After finding how to track the movements of alleged CIA planes used for rendition, he published the first flight logs of these jets in the Sunday Times in November 2004. He went on to contribute to several front page news articles to the New York Times about rendition and security issues, as well as to Newsweek, CBS 60 Minutes, Le Monde Diplomatique, and BBC Radio 4's 'File on Four'. He presented television documentaries on the CIA rendition program for Channel 4's Dispatches Program and PBS Frontline World.
In 2005 he received the Amnesty International UK Media Award for best article in a periodical, for his New Statesman article.
In 2006, he received the Joe and Laurie Dine award for Best International Reporting in any medium dealing with human rights from the Overseas Press Club of America. The citation described his book, Ghost Plane, as
the consummation of years of investigation, not only by the author, but, as he acknowledges, the informal global network of journalists with whom he collaborated to reveal the murky world of rendition, extraordinary rendition and proxy torture. By tracing the landings and takeoffs of clumsily concealed CIA flights, his work not only demonstrates concerned investigative journalism in action, it lifts the lid on a global gulag of prisons and torture chambers, assembled by US officials in defiance of domestic and international human rights law.
In a broadcast on the BBC World Service on December 30, 2009, reviewing the last ten years of journalism, author and campaignerHeather Brooke described Grey's investigation of the CIA rendition flights as the "journalistic scoop of the decade."