The two shells were connected by a bridge. The Big Shell balanced itself by attaching shell struts to the shell core. If both shell cores were to be destroyed at the same time, the entire facility would collapse. Most of the functions and layout were given out in a brochure.

The Shell 1 Core is one of the more important facilities, and it was the centre of the Big Shell: Its first basement floor contained a meeting hall that was used for the receptions for the President as well as the environmental protection inspection team. Because of it being used by high-ranking officials, it also contains biometrics scanning equipment at the door to the meeting hall. A break-room is also situated nearby. The second floor basement contained a computer room that was used to monitor the flow of polluted water and the status of filtration, as well as where all tasks of the Big Shell are carried out. Presumably, the computer room also was the location where GW was being programmed, which made security in this area very tight. The second floor basement also contained a large door that led straight into Arsenal Gear. 

Strut A contains a pump facility to supply energy for the circulation of polluted sea water into the sections of the Big Shell, although the pump facility itself was actually congregated in the southern section of Strut A. The controls for the pump facility were located in the northern section of Strut A. Strut A also contained a dock that was used for deep sea submarines to investigate for damages around the Big Shell underwater.

Strut B acts as the electric generator for the entire facility, with its power substation being located on the first floor.

Strut C is the residential area of the facility, which contained a kitchen, a pantry, restrooms, and a mess hall to support the few workers it has.

Strut D contains sediment pool no. 1, which was a facility where polluted water was stored without disruption so that its large pollutants could settle and then be extracted from the water.

Strut E contains a heliport, which was used as an aerial transport hub to deliver supplies to the facility due to the oil fences surrounding the Big Shell cutting off its sea entrances from seafaring transport vessels. Inside, Strut E contains a conveyor system that transports supplies throughout the different areas of the facility, to which it sorts the supplies to where it needs to go via the markings of its containers.

Strut F acts as a warehouse for several of their equipment that they didn't have any immediate use for.

The Shell 2 Core was where the actual filtration system resided. It purified the waters via benign bacteria in the area that broke down the oil in the water via microbes decomposing microcarbons. The area below the first floor contained a vat for this purpose. As a side-effect of the microbes decomposing the oil by absorbing large amounts of oxygen in the purification chamber, the water within the chamber also had its buoyancy virtually eliminated, which meant there was virtually no chance of getting back to the surface once one falls into the vat. The first floor also contained an air purification facility that eliminated the stench from the seawater that resulted from the oil spill. However, the vat broke at some point, causing the shell to flood in areas below the first floor.

Strut G contains the oil processing facility. This is likely similar to strut D.

Strut H contains a warehouse which is was likely used to the same extent as Strut F.

Strut I contains an assembly facility. It also contains a Helipad which indicates that its purpose is similar to that of Strut E.

Strut J contained a power plant, which is likely used to produce power for the whole facility similar to Strut B.

Strut K contains a biochem lab which was likely similar to Strut A.

Strut L contained the effluent processing facility, which treated sea water that was expunged of oil was treated with chlorine and other chemicals to sterilise and disinfect the sea water so it could be made suitable for flushing back into the ocean again.