2008–2013: Further writing, producing
McQuarrie first met frequent collaborator Tom Cruise, seeking simply to unload a screenplay in order to pay his debts and exit the film industry. This screenplay, co-written with Nathan Alexander, later turned into Valkyrie, which opened on December 25, 2008, and would also be the first film where McQuarrie served as a producer. The film is based on the real-life July 20, 1944 plot to assassinate Adolf Hitler. While researching the screenplay, the writers had access to members of the Stauffenberg family; consulted a book written by Fabian von Schlabrendorff, a conspirator who survived; and spoke with Hitler's surviving bodyguard. The film, directed by Bryan Singer, received the BMI Film Music Award and the Bambi Award for Courage. McQuarrie initially only took a producing credit on the film for its associated pay increase. But, after a conversation with Paula Wagner, whose increased commitments with United Artists left little time for creative collaboration with Cruise, he decided to fully involve himself in the film's production, as well as replace Wagner as Cruise's primary creative partner.
In 2009, McQuarrie was hired to pen the script for the then-untitled The Wolverine. He also co-wrote the 2010 film The Tourist with Julian Fellowes, Jeffrey Nachmanoff and director Florian Henckel von Donnersmarck. It starred Johnny Depp and Angelina Jolie and grossed US$278 million worldwide. It received three Golden Globe Award nominations and several other awards, among them the Redbox Movie Award for the most rented drama of 2011. McQuarrie then provided uncredited rewrites on the 2011 action spy film Mission: Impossible – Ghost Protocol during the film's production.
In 2011, McQuarrie directed his second feature, Jack Reacher, an adaptation of One Shot, the ninth in the series of 21 Jack Reacher novels by Lee Child. Filming began in the Pittsburgh metropolitan area on October 3, 2011, and continued through the end of January 2012. The movie was released in December 2012 by Paramount Pictures. In 2012, McQuarrie stepped in to rewrite the script for World War Z after Drew Goddard and Damon Lindelof left the film.
2013 saw the release of McQuarrie's fourth collaboration with Singer, Jack the Giant Slayer, co-written by McQuarrie. Critical reviews were mixed, and it was a box office failure, grossing only US$198 million against an estimated US$240 million budget (excluding promotion). McQuarrie co-wrote the 2014 science fiction action thriller Edge of Tomorrow with Jez and John-Henry Butterworth, based on the Japanese novel All You Need Is Kill.