An older idea of mine that I’ve fleshed out a bit more. It all begins in 1960 when Jack Ryan failed to find the solution to the genetic conditioning that was commanding his body to stop his heart from beating. With the city under his control, Frank Fontaine established almost total control over the ruins of Rapture but that wasn’t nearly enough anymore.
With the bathyspheres now available to him, Fontaine returned to surface, abandoning the dying city, taking anything he saw of value with him and heading back to the mainland USA. His only remaining presence in Rapture was around the old fisheries from which he could send submarines out to harvest more sea-slugs for ADAM. With Fontaine gone Sofia Lamb’s utopian communist sect took over most of the rest of the city’s ruins and conducted their own experiments with the remains of Rapture’s technology.
Fontaine proceeded to take his operations back to the USA, hiding away his splicer hench