During the early events of Deus Ex, Bob Page donates a new submarine pen to the facility, and later in the game, Majestic-12 moves the PRCS Wall Cloud superfreighter into its pen. The Wall Cloud is carrying several hundred tons of the Gray Death nanovirus, and is heavily guarded by security cameras, various bots, and countless soldiers of American, Russian, and Chinese nationalities.
The shipyard can be divided into 3 different areas: a front gate blocking a courtyard of mostly deserted office buildings, the sub pen itself, and several heavily guarded warehouses and courtyards between the two. The soldiers at the front gate aren't hostile to the player, and will open the gate for them if they had talked to Vinny in Hell's Kitchen.
The central warehouses contain several soldiers and a few Bravo-3 Peacebringers - the player may stop here to pick up LAMs if they don't have enough explosives to scuttle the freighter. The final courtyard is patrolled by Delta-2 Peacebringers, and the player must pass through here to get into both the sub pen's ground level entrance and the crane leading to its ventilation shafts.
A sewer system runs under the entire shipyard, though it is guarded by several turrets and laser tripwires. The Sub Pen is guarded by Russian Sailors and Chinese Military, both on the dock and on the ship itself.