Fury's investigation leads to more questions than answers. The agents believed to have been killed during the Delta Affair (see the "Nick Fury Vs. S.H.I.E.L.D." 4 part miniseries) were not killed, but were instead kept in stasis for another plot on another day. Quartermain was restored physically, those his memory is not his own, and he's now working for Hydra. Fury doesn't realize that there are other Hydra agents working with him on a daily basis.
