So, there's a post of here that claims the time gap between Crysis 2 and Crysis 3 is because Prophet (Alcatraz, who later took on the name at the end of C2) was imprisoned. Well, during Crysis: Legion Alcatraz is questioned about the Ceph-Human War by the CSIRA BlackBody Council. Though if this is true, I wonder how a supersoldier was imprisoned, unless of course when he was being arrested they had an emp or k-volt, just anything that would disable the nanosuit.