The Hijacking and Retaking of the Lemurian Star was an event that marked the beginning of the HYDRA Uprising.
Nick Fury became suspicious about the real purpose of Project Insight and secretly hired Georges Batroc to hijack the Lemurian Star. Jasper Sitwell was ordered to board the vessel by Victoria Hand, taking him away from assisting in the search for the Clairvoyant.
Captain America was trying to adjust to the present and its politics by moving to Washington, D.C. and listening to Black Widow's suggestions.
Unbeknownst to S.H.I.E.L.D., HYDRA had been planting secret double-agents in the organization for decades.