Constructed by the former president of Shinra, the Deepground is a specially created group of SOLDIERs who work against WRO in their plan to call forth the last WEAPON, Omega.
History
Some time before Meteorfall, President Shinra developed plans to create a super-human race who would become the ultimate warriors in SOLDIER: terribly powerful fighters, all but emotionless and without a sense of morals. His plans come to fruition in a research facility deep below Midgar. Given the nature of the project, only the highest ranking officials in the government know about its existence -- and the existence of the SOLDIERs themselves.
Originally, Deepground was a medical clinc where injured soldiers would be sent for rehabilitation and treatment. However, because of a mysterious man known only as "G", the medical clinic became a twisted laboratory that used its patients in immoral genetic experiments. The results of these experiements were a new breed of super-SOLDIERs.
All around Gaia, people are collected for the experiment, including one Shelke Rui, younger sister of Shalua Rui. Both the minds and the bodies of the test subjects are manipulated, and they are subjected to terrible tests that would challenge both their newly developed skills and reworked mindset. Still, despite the project's goal to erase their emotions and morality, the SOLDIERs' memories linger at the fringes of their conscious minds.
As the pre-Meteorfall events cause President Shinra and his executives to turn their heads to more pressing matters, the Deepground SOLDIERs and the project they're a part of are put on hold. One by one, President Shinra, Scarlet, Heidegger and Hojo are killed, and the knowledge of the project goes with them to their deaths.
After the president's death, the transfer of power to his son was carried out so quickly, I doubt Rufus was ever briefed on the project.
Quoted by ReeveEven though Reeve was a high-ranking official, it was decided he didn't need to know about the project, given his status as head of urban development -- a job not exactly linked to warfare and all matters that concern it.
Development
For three years, the Deepground was trapped beneath the ruins of Midgar, forgotten. Those living in Edge, the city that was once Midgar, tell tales of hearing screams coming from the city's ruins. When a team goes to investigate, none come back.
The existence of the Deepground first becomes known through a collection of files deceased Shinra executive Scarlet left behind. It's not long until the real deal arrives in a terrible display of violence against the town of Kalm. In particular, the elite group of Deepground SOLDIERs, the Tsviets, make their presence known. Reeve and the WRO work with Vincent Valentine to save the town, and although they succeed, much damage has been done.

























