Full Synchronisation Requirement - Do not be detected.
The easiest way to get your hands on Sofia’s package is to head around the back of the restricted area and climb onto the ship that way. Go to the coastline without heading into the restricted area and dive into the water from a rooftop, being careful of the riflemen on the rooftops as always.
Head around the back of the ship and try to take out one of the patrolling guards with a low profile ledge assassination. Then, climb up and assassinate the remaining Templar before switching to Eagle Sense to try and find the right package. It’s the one on top of the crates on the upper deck area of the ship, if you’re having trouble.
Once you’ve examined it and picked it up, either dive off of the ship again and swim back the way you came, or alternatively try and sneak onto the rooftops inside the restricted area and make your way out of the search area on the minimap. Once you’ve delivered the package to Sofia, the memory will end with a cutscene.