The aft cargo hold has been the main focus of site investigations since the late 1980's. Following several years of litigation and permitting procedures, SJAEI began an intrusive investigation in 1988. After an attempt to find a cargo hatch failed, a hole was cut through the deck to gain access to the interior spaces (Figure 19). Excavation continued in the same area in 1989. Material recovered from the hold during the two year project provided the circumstantial evidence to prove the Maple Leaf's identity. Following a two year hiatus on field work, the entrance hole was re-excavated in 1991 to monitor interior conditions. It was opened again in 1992 to take water samples for analysis (Cantelas 1992:13-36, 1993:14-17).

Previous work in the cargo hold created a sloping trench extending down from the port side to the centerline of the vessel. It measured approximately eight feet long and six feet deep. This trench provided a working space and starting point for the 1993 investigation. A decision on the excavation's final direction was made after considering research goals in conjunction with examining the condition of the material in the trench walls.

The primary goal was the controlled recovery of packing containers and their contents to interpret the material record of the Civil War as represented by this site. It also provided the opportunity to study how the vessel was packed which reflects the stevedoring practices used during the mid 19th-century. Finally, the open space created inside the hull provided a chance to examine interior construction. Examining material exposed in the walls revealed a high artifact concentration in the southeast corner. Extending the excavation in this direction, towards the bow and centerline of the ship, offered the best possibility to answer research questions on material culture and ship construction. The resulting field investigation generally proceeded on an east/west line under the centerline of the ship. The small hole SJAEI cut in the aft deck in 1988 was enlarged in 1989 to measure approximately 8 feet long, athwart ship. Removing a deck beam from the center of the narrow hole, created an opening 42 inches wide. The opening is the only known entrance to the cargo hold and provided access in 1993. It is located 139.5 feet aft of the bow and begins at the centerline of the ship and extends toward the port side (Figure 20).