In the last episode S01E16 of Marvel's Agents of S.H.I.E.L.D., it is revealed that
Agent Victoria Hand is a villain. She is either Clairvoyant herself or she is working for him. She is a high-level S.H.I.E.L.D. agent to order Melinda May for secret reports.
Mike Peterson clearly didn't kill her (Coulson's reasoning looks correct) and Victoria Hand changed course of the airplane after the encrypted line became disabled, but...
Previously in the show, when Agent Coulson told Skye about the alien (using which GH-325 was made), Melinda May intercepted it and reported it to someone: "He knows. I repeat, Coulson knows."
It says that the other person on the other side knows about the alien thing. I thought she reported to Director Fury. But, how could she report in such a way to the villain side which didn't know anything about the alien and the drug (Fury kept it secret; just to know about the secret they kidnapped Agent Coulson and injured Skye)?
Where's the catch?