In an effort to save humanity from the eventual melting of polar ice caps and overflooding, ex-WayneTech employee turned self-employed geneticist Professor Anton Geist theorized the creation a strand of DNA that would convert the respiratory, auditory, ocular and muscular systems of humans into a more marine-based model to allow them to live underwater.
Progene Tech, a subsidiary of energy giant Arbiston Global (which was funded and run by Vandal Savage), learns of Geist's theoretical research through an old workmate of Geist's, Gregory Jupiter, and secretly funds his theory's development.
Completing his research, Geist creates his serum using a sample of Aquaman's DNA and further develops it to only become active when a sudden infusion of salt water is introduced to the affected subject before secretly introducing the serum into the city's water supply three years, ten months and seventeen days before the earthquake.
Supporting the plan to forcibly drop part of the city underwater to further his "life-saving research", Geists helps in the development of several Lithophage mutants; artificially created monsters that burrow into the Earth's crust and precisely eat away at the edges of the tectonic plates until they slip and cause an earthquake that leaves 400,000 persons recorded dead or missing and everything west of the San-Diego Zoo underwater. Despite patrolling the underwater wreckage, Aquaman reports that he had found no survivors.
One month after the earthquake that Sub-Diego inhabitants come to refer to as "The Fall", President Pete Ross announces on-stie that no cause for the quake was found aside from natural causes.
Days after the presidential speech, and five weeks after the earthquake, a young boy appears and walks onto the beach from the ocean but dies due to suffocating in the air.
After analyzing the boy's body Aquaman removes part of the memorial wall, which skirted the edge of the city's newly defined coastline, and announces the survival of water breathers within the submerged part of the city. Immediately during this announcement, Lorena Marquez surfaces and is saved from suffocating by Aquaman and Martian Manhunter.
While helping the people underwater, Aquaman and Lorena discover a Lithophage; an artificial creature that was emitting a low frequency that was similar to a frequency that was emitted during the quake. The Lithophage was created by Progene Tech to burrowing into the Earth's crust and precisely eat away at the edges of the tectonic plates until they slip and cause an earthquake.
Dogs begin waking up and attempting to return to the surface but are blocked and thrown back into the ocean by the populace of San Diego to prevent them from "drowning" in the air.
While this is happening Aquaman and Lorena track the creator of the Lithophage to Professor Geist and force him to live in Sub Diego as penance for his involvement in the earthquake.
Six weeks after the earthquake, the first baby is born in Sub Diego, however, it did not posses the ability to breath underwater and Aquaman had to bring it to the surface to breath and so Aquaman employs Geist to find a solution to the problem of babies being born as air breathers, creating an underwater laboratory for the Professor to work in.
As Sub Diego evicts itself from the San Diego council to operate independently, The Eel (Mort Coolidge) attempts to take over the city's criminal element with his telekinetic power but is defeated.
After consulting with the most powerful members of the JLA and the JSA on whether it was viable to pull Sub-Diego back to the surface, the US Government employs the Sea Devils to aid Aquaman in retrieving weapons trapped within the military facilities in Sub Diego. They meet and fight Marauder as he is attempting to plunder the weapons.
Ned Moriarty begins trading heroin and cocaine in Sub Diego but is thwarted by Aquaman.
Using the bones of Aquaman's amputated hand, Ocean Master alters reality around Sub Diego and switches places with his brother; making himself Aquaman and Orin as The Ocean Master. However, Geist remained unaffected by Ocean Master's spell and managed to remind Orin of who he really was; enabling Orin to break Ocean Master's spell and retrieve the bones of his hand.
Three months since it fell in the ocean, after getting phone lines established between the cities, San Diego begins organising glass-bottom boat tours over Sub Diego to allow people to see each other.
Geist turns Captain Alonzo Malrey into a human-shark hybrid to help police Sub Diego.
After observing the goings ons in Sub Diego closely, and believing Geist dead, Progene Tech's chairman, Gregory Jupiter, announces that they have patented Geist's mutation formula.
Envoys from Atlantis arrive at Sub Diego in an attempt to get Aquaman to return to ruling Atlantis.
Chandra Abbott has a psychotic break and begins murdering Sub-Diego citizens by breathing oxygen into their lungs. While investigating the case Aquaman re-establishes the city's police force.
Arbiston Global begins building pipelines in Sub Diego to syphon thermonuclear energy from seafloor volcanic gas vents.
Feeling ostracized in Atlantis, Koryak returns to Sub-Diego with Lorena after the two meet during an exhibition between the two cities.
Geist starts having momentary blackouts as the OMAC nanites within his body record what he sees. As Aquaman comes to Geist with Mera in an attempt to reconvert her into a water breather again, Brother Eye activates its OMAC army in response to Wonder Woman killing Maxwell Lord and Geist transforms into an OMAC; attacking Aquaman before being killed by Koryak.
Meanwhile Progene Tech successfully administers Geist's formula to Black Manta, who then breaks out of their labs and amasses a group of aquatic supervillains to attack Aquaman at Sub-Diego as the Spectre attacks Atlantis.
Following Atlantis' destruction, Atlantean refugees are transported to Sub Diego as supplies are flown in from the surface.
During the time surrounding Black Adam's rampage around the globe, Geist's formula begins wearing out and people begin drowning within Sub Diego. In an effort to save everyone, Aquaman makes a deal to gain enough magical power to raise the city back above the ocean but is turned into a monster in the process.
Known as "The Rise", Coronado and Point Loma remain underwater where the remaining water breathing citizens rebuild.
Hotel Del Coronado becomes the new town hall.
Tempest appears in Sub-Diego, amnesiac and now only able to breath air.
Cal Durham becomes the new mayor but after he leaves for Poseidonis to request help in rebuilding, Black Manta comes in a forcibly takes over the city as part of a job for Progene Tech to gain as much genetic samples of the city's water breathers as possible before he is defeated by Joseph Curry.
Tracing his employers back to Progene Tech, Joseph Curry, Quagirl and Cyborg are just in time to stop Vandal Savage and Krusivax's plan to sink the Pacific Rim.