The construct itself is a sentient refugee camp, henceforth referred to as the Sanctuary, created by an unknown party to be used as a safe haven for potentially globe-spanning populations fleeing from potentially globe-spanning catastrophes. The Sanctuary, like most refugee camps on Earth, is meant to serve as temporary shelter for these populations before a suitable safe environment can be found for the refugees to settle. Upon entry of a new occupant (or "refugee"), it probes the mind and biological makeup of the refugee to determine its basic needs by parsing the information acquired. As more refugees enter the Sanctuary, it expands outward so that there is sufficient space to house and contain its occupants, and creates new points of entry to ease the flow of refugees into the first-used entrance. From that point forward, the Sanctuary will begin operation of numerous processing facilities to provide for its inhabitants' needs. As refugee camps are temporary settlements by design, these processing facilities strictly produce the needs of its inhabitants, both tiding the refugees over while searching for resettlement locations, and to discourage permanent residence within the Sanctuary — something antithetical to the Sanctuary's nature as a temporary settlement. It is theorized, however, that upon locating a suitable world for a population's resettlement, the superfactories will finally turn on and start supplying the departing population with equipment and resources to begin the rebuilding of society, as well as potentially producing their long-desired wants.
As with most refugee camps on Earth, however, it is seldom easy to leave once you're in. While refugees want to go home, and the camps need to be emptied, there are few locations that will accept them — or, as is sometimes the case with the Sanctuary — that are best suited for their biological needs. Furthermore, their homelands are rarely willing or even able to welcome them back, if they exist anymore at all. As such, the Sanctuary has taken it upon itself to provide for the refugees, often keeping them within its confines against their will. This places its inhabitants in a state of limbo — no longer belonging to any particular nation-state, only bound together by either their shared heritage in the case of intraspecies relationships, or by their shared home within the Sanctuary, in the case of interspecies relationships. The Foundation has discovered numerous populations both above and below the first-discovered region of the Sanctuary, all in a state of forced cohabitation due to their varyingly prolonged stays within.
The Sanctuary is known to take in ONLY those it can determine to be "refugees", thus, in order to properly explore it, the Foundation has had to "make" refugees of its own via extralegal means and enlisting them as D-class personnel — one of many matters that should concern the Ethics Committee.
As the nature of the SCP Foundation is to Secure, Contain, and Protect, the securing and classification of the Sanctuary raises ethical concerns, specifically in regards to hiding from the public a refugee crisis of an interdimensional scale. Additionally, despite early failed attempts to rescue a handful of refugees, the Foundation views the acceptance of these refugees onto Earth as a potential containment breach, and has chosen to keep the refugees from leaving, ignoring their wishes to leave and effectively assisting their captor (the Sanctuary). This raises the question of whether it is morally correct to harm other species/civilizations from other worlds in order to maintain normalcy on our own world.
Furthermore, with the continued influx of D-class personnel, be they former refugees themselves or not, the Sanctuary has begun accepting all D-class personnel into its construct as refugees, creating an anti-containment breach; where the Foundation experiences a net increase in things contained as the Sanctuary comes to understand D-class as refugees being hunted by the very Foundation they work for. In response, the Foundation begins severely limiting access to the Sanctuary, attempting to bar D-class personnel from entry. This has effectively placed the Foundation on the moral low ground, and henceforth requires special review by the Ethics Committee.
So, yeah. There's my idea. I'll happily accept feedback, critique, questions, and suggestions. I'd like to thank DrAstari for helping me get the idea actually down proper in its current state, and to Nytlaz and RTME for helping properly form the narrative from its many hooks.