The ship is comprised of two main areas: the upper decks and lower decks. The upper deck is accessible via three different routes. It can be boarded using a ramp on the starboard side of the ship that is initially retracted. The ramp must be lowered using a nearby Security Keypad before it can be used as an entry-way. Alternatively, JC can take an elevator to a room which controls one of the cranes; the crane can be moved into a position that allows him to jump directly onto the ship. The third option is to climb a ladder on the port side of the Wall Cloud (which must be swam to).
Once on board, JC has to navigate the upper decks before he can enter the lower decks. This part of the ship contains a chemistry lab (where a vial of Ambrosia can be found), crew quarters, a sick bay and the ship's Command Center. The nanokey unlocking the door to below decks is located in the Captain Zhao's Quarters, as well as a holocomm with a message from Walton Simons.
Once below decks, JC needs to locate and destroy the 5 tri-hull welds. Two are found in the engine room, one in electrical, one in the bilge pump room and the last in the helicopter bay. Additionally, the computer in the bilge pump room must be accessed in order to reverse the flow of the pumps.