Looking back at JJ Abrams and having read some of the comics, one of my deepest fears may be coming true. A number of his works involve a conspiracy, which the protagonists must identify and confront.
In the comic "The Return of the Archons", it was insinuated that there is a conspiracy involving Starfleet. Admiral Pike is aware of this and is in contact with one of the conspirators. He is told by his contact to keep Captain Kirk in check. In the comic, the captain had uncovered an experiment on Beta III that was initiated by Starfleet. Now, from the Empire Magazine, the readers are informed that "He’s an incredibly brilliant strategist who is aware of various truths that Kirk is not privy to