star trek into darkness AU:
john harrison is really john harrison, rogue starfleet agent
Commander John Harrison, bioengineer and science officer of the U.S.S. Reliant, is recruited by Admiral Marcus to Section 31 after his crew discovers the wreckage of the Botany Bay while on a routine exploratory mission in deep space. His assignment is to study and recreate the genetic enhancements made to the Bay’s crew during the Eugenics Wars, and he pursues this goal with enthusiasm, even performing several of the augmentation experiments on himself. Things take a turn for the worse when Starfleet begins to confiscate Harrison’s research, piece by piece, until the day his clearance is suddenly revoked and a team of operatives attempt to take him into custody (he is, after all, one of his own test subjects). Harrison escapes, then subsequently disappears, a fugitive from the Federation, only to resurface months later when he destroys Section 31’s London facility and stages a one-man assault on a meeting of Starfleet’s highest-ranking officers. When the Enterprise discovers and captures him on Kronos, an unlikely and reluctant alliance forms between Harrison and Kirk to stop Marcus, the man who used them both, from beginning an all-out war between the Federation and the Klingon Empire.