She then joined The Guardian as a political correspondent, presenting the newspaper's 'Politics Weekly' podcast with Tom Clark. During this period she wrote the novel Muhajababes, which explores the youth culture of the Middle East, which addressed the contradictions of modern life of young adults in Muslim societies.
Stratton returned to the BBC on 20 February 2012, as political editor of Newsnight, replacing Michael Crick who left to become a political correspondent for Channel 4. There was criticism of an interview by Stratton broadcast on Newsnight on 23 May 2012. Stratton interviewed a woman, Shanene Thorpe, whom The Independent later reported to have been "fuming" because (it was asserted) the piece was edited (though not by Stratton, who was not the editor) to make her seem like a 'jobless ponce' whereas she did in fact have a job.Peter Rippon, the responsible Editor of Newsnight, later apologised in an open letter to Thorpe, accepting that someone could have got the false impression she was unemployed.