Plugging nicely into the RPG world of Delta Green, Rough Magik is about The Night Scholars, a clandestine organization setup to monitor the ancient cult of Cthulhu. After decades of compiling an enormous database of arcane information, they have come to a single, incontrovertible conclusion: the Sleeping God is waking. Diana Armitage, with the help of her Home Office liaison, the mysterious Mr. Moon (Paul Darrow), launch an aggressive campaign against the Dreamers. This operation, designated the Rough Magik initiative, was successful but they trod on the toes of some powerful people, amidst accusations of financial impropriety and possible treason, and the Night Scholars were disbanded. Now years later, the old magic is returning, the Sleeping God is rising, and there are more Dreamers than Mr. Moon can handle as he struggles to rebuild the Night Scholars before its too late.

Michael assists Nikita on one of her missions, and Alex suffers a panic attack during basic training.