James Howlett is a mutant who has been alive for over a century. Over the years, James's mind has undergone numerous traumas, including scientific tampering by clandestine organizations, which have made it impossible for him to remember his true past. What he is left with is bits and pieces of memory and no way to tell when, and if, many of the events actually took place.
What is clear is that, prior to the Mutant-Human War, James, codenamed Wolverine, was a key operative in the S.H.I.E.L.D. organization. Trained by some of the best military men on the planet, including Nick Fury and Frank Castle, Wolverine was used in only the most covert of operations. Because his superiors knew of his Mutant nature, he was kept away from the Mutant-Human War. It was only when the war was all but lost that his superiors decided to brainwash Wolverine into carrying out an assassination attempt on the mutants' leader, Magneto. The mission never took place. With mutants victorious, S.H.I.E.L.D. was temporarily shut down. James was released from his solitary quarters and discovered a brave new mutant world.
As S.H.I.E.L.D. was restructured by its new Director, Sebastian Shaw, Wolverine was placed in charge of a special squad of mutants known as the Red Guard. It was here he met his current lover, Mystique. The Red Guard has been used almost exclusively to hunt down human terrorists and superhuman threats. It has been more than up to the task with a 100 percent success rate. With family and friends, and a new place in the world, James was finally content.
Unfortunately, things have changed. James has begun to have nightmares causing him to question his own life and the world itself. He has attempted to drown these with alcohol and painkillers but this has proved unsuccessful. Though he hates the idea of anyone "mucking" around in his head, he even turned to the S.H.I.E.L.D. telepaths for help, but they failed.
These images have become more visceral and have led Wolverine to make some questionable decisions in the field. Those decisions have led Sebastian Shaw and his team, including Mystique, to question Wolverine's sanity and future role in S.H.I.E.L.D.