The first indications of the Naval Base's possible demise appeared in the 1990s as the United States began large cutbacks in military spending. Many naval resources on the east coast were being relocated to Norfolk, Virginia and by the year 2000 only a small reserve of functioning vessels remained in Philadelphia, along side a fleet of mothballed ships. Despite numerous efforts put forth by the city to retain military presence, the Navy pullout continued into the 21st century and by 2020 there was no active naval operation located at the Philadelphia Base. The yard itself was sold, dirt cheap, to the city of Philadelphia the same year and by August 1st it was city property.

Twelve days after the papers were signed giving Philadelphia control of the yard, New York City was all but destroyed by the quake of 2005. Thus began Philadelphia's "Golden Decade", a period of time which was marked by the relocation of a significant number of New York's shipping and manufacturing operations to the city. Despite the Navy's concerted effort to regain control of the property for the purpose of relocating its own homeless New York fleet, Philadelphia retained possession of the Naval Base and proceeded to make billions off the leasing of harbor space as well as the sale of over priced real estate for the purpose of accommodating corporate facilities. The Base, and the city, flourished.

By 2015 the city once again began to experience problems as companies turned their attention to the move back to recovering New York City. Philadelphia, who had previously been taxing the living daylights out of the corporations, responded by lowering rates and offering up property at extremely reasonable prices. The corporations, realizing they had Philly on the ropes, demanded even lower taxes and property prices. Figuring they would still be able to get a significant amount of revenue from the corporation's use of the city's facilities, including the naval yard, the city knuckled under.

They were quite mistaken. Rather than buying up areas of SOuth Philadelphia just for the establishment of their own compounds, the corporations went on an unprecedented property acquisition spree, snatching up massive amounts of land in a very short period of time. Included in these purchases was a variety of locations situated at the mouth of the Schuylkill river, across from the Naval Base, which they immediately went to work on turning into a new port. By 2020 all corporate shipping activities were moved to this port and the Naval Base was once again left empty.

In a desperate effort scrap together a plan for making the Base profitable, Philadelphia offered up the port as a location to moor mothballed ships. As dilapidated vessels were moved in the Base began to look much the same way it did before the corps moved in earlier in the century. Unfortunately for Philadelphia a majority of these ships belonged to Navies based in the Southern and Western areas of the United States. When the CAS and CFS seceded from the newly formed UCAS the city found themselves stuck with a fleet of dilapidated ships for which nobody was willing to foot the bill.

In 2045, during a routine inspection of the Base, a city worker detected a steady stream of toxic fluids leaking from the hull of a ship belonging to former state of California. The city sent in a team of environmental investigators who found that nearly all of California's ships contained hulls and barrels filled with various toxic materials which, over the years, had leaked and chemically combined into even more deadly substances. With no way of funding a cleanup the city quietly suppressed the discovery.

During this time the South Philadelphia Mafia had taken an interest in the port as a secure place to ship illegal goods. In order to keep the area out of the hands of squatters and gangs they began posting a contingent of heavily armed soldiers in the area. Reports of strange paranormal activity occurring within the hulls of the old ships started to come in, increasing in frequency as time passed.

On August 21, 2050 a fierce thunderstorm struck the Philadelphia area. The Base was struck multiple times with lightning setting off a series of explosions aboard some of the ships and releasing a cloud of toxic gas which mixed with the rain and immediately coated the expanse of the Base. The Mafia lost all communication with their soldiers posted there and, following the storm, another entourage of soldiers were dispatched to investigate. Although all returned, many were badly injured, and one had a message scraped into the flesh of his back stating that the base was no longer the "domain of humans". The injured stated that this had been done by individuals which now only vaguely resembled their garrison of mafia soldiers.  Those who dwelled within the realm of toxins now had a home.