On July 4, 1994 he wrote an article about Kevin Mitnick, who was then a fugitive from a number of law enforcement agencies. He wrote several more pieces detailing Mitnick's capture. Markoff also co-wrote, with Tsutomu Shimomura, the book about the chase. The book later became a film that was released direct to video in the United States. Markoff's writing about Mitnick was the subject of criticism by Mitnick supporters and unaffiliated parties who maintained that Markoff's accounts exaggerated or even invented Mitnick's activities and successes. Markoff stood by his reporting in several responses. The film went much further, with Markoff himself stating to the San Francisco Chronicle in 2000, "I thought it was a fundamentally dishonest movie." Markoff was also accused by Jonathan Littman of journalistic impropriety and of over-hyping Mitnick's actual crimes. Littman published a more sympathetic account of Mitnick's time as a fugitive in his own book on the incident, The Fugitive Game. Further controversy came over the release of the movie Takedown, with Littman alleging that portions of the film were taken from his book The Fugitive Game without permission. Markoff's involvement with Mitnick is thoroughly covered in the documentary Freedom Downtime, in which an interview is conducted with Markoff who is unable to elaborate on the veracity of Mitnick's charges.
Post-Mitnick
After Mitnick, Markoff continued to write about technology, focusing at times on wireless networking, writing early stories about non-line-of-sight broadband wireless, phased-array antennas, and multiple-in, multiple-out antenna systems to enhance Wi-Fi. He covered Jim Gillogly's 1999 break of the first three sections of the CIA's Kryptos cipher , and writes regularly about semiconductors and supercomputers as well. He wrote the first two articles describing Admiral John Poindexter's return to government and the creation of the Total Information Awareness project. He shared the 2005 Gerald Loeb Award in the Deadline Writing category for the story "End of an Era". In 2009 he moved from the Business/Tech section of the New York Times to the Science section. Markoff contributed to the New York Times staff entry that received the 2013 Pulitzer Prize for Explanatory Reporting. The series of 10 articles explored the business practices of Apple and other technology companies. He retired from his full-time position with the New York Times on December 1, 2016. He continues to work as a freelance journalist for the Times and other organizations and volunteers at the Computer History Museum. Markoff is interviewed in Do You Trust This Computer?, a 2018 documentary on artificial intelligence.