It could be a rogue organization within S.H.I.E.L.D. that has gone bad. They might want to use Hawkeye to get rid of the Avengers because they see them as too powerful and uncontrollable. This organization could have access to some new technology or magic - like artifacts that they use to brainwash Hawkeye and turn him against his friends.
Loki could be a likely villain. He has a history of mind - controlling people and causing chaos within the Avengers. He might see Hawkeye as a useful tool to disrupt the team again. His mischievous nature and magic powers would make it easy for him to brainwash Hawkeye without being detected at first.