From the Metal Gear Wiki

The Big Shell is the main area used in Metal Gear Solid 2: Sons Of Liberty. It is taken over by Olga's Mercenary army, as well as members of Dead Cell under the command of Solidus Snake.

The Big Shell is shaped like two hexagons connected end-on-end. At the centre of each "hexagon" is a Core (Core 1 and Core 2) each core is surrounded by six lettered Struts (Core 1 is surrounded by Struts A to F, Core 2 surrounded by Struts G to L.) Each Strut serves a different purpose though most of the one's from Shell 2 are unknown, until you get to the Strut L perimeter. The Struts are all connected via. a series of bridges, each linking to each other, and some of the Bridges that link to the Cores (for example the Bridge linking Struts B and C also links to Core 1) The two Shell's are connected by a bridge between Struts D to G.

When the Tanker Discovery sank, The Patriots decided this would be a good time to start work on Arsenal Gear. So they quickly sent another tank filled with Oil to the spot where the tanker sank, and proceeded to sink this tanker. They then quickly placed a gigantic Oil Fence around the site and built the gigantic Oil Clean-Up Facility and codenamed it the Big Shell. Of course this was all a cover up, under the facility The Patriots secretly developed Arsenal Gear.