Board Thread:General Discussion/@comment-74.141.212.63-20140904140257/@comment-5244881-20140906101123

That Hydra/SHIELD storyarc started with Captain America: The Winter Soldier, continued with Agents of SHIELD and Avengers: Age of Ultron and will probably be ended in Captain America 3, so I don't think there will be any remaining parts of Hydra left in Thor 3.