Multiple realities
(covers information from several alternate timelines)
"The indigenous race abandoned this planet long ago. They left behind sophisticated mining equipment and a drone workforce. They have some kind of technology that prolongs life."

The Ancient Ones were a civilization indigenous to the planet Altamid up until the 22nd century, when they abandoned the planet.

Among the technology created by the Ancient Ones was a bioweapon called the Abronath, a massive fleet of Swarm ships (as well as drones to pilot them), and equipment capable of rejuvenating the user through energy transference, forcibly draining the life from another person and assimilating some of the victim's DNA in the process.

When the USS Franklin crashed on Altamid in 2164, the three survivors – Balthazar Edison, Anderson Le, and Jessica Wolff – found the Ancient Ones' cache of technology and began using it for their own purposes, raiding passing ships to capture and drain their crews while searching for the missing half of the Abronath. (Star Trek Beyond)

Based on the design of the structures on the planet and the appearance of the Swarm drone, it is likely the Ancient Ones were humanoids. Presumably they were also responsible for the subterranean development of the planet.
Director Justin Lin referred to them as "Altamidians". [1]
Star Trek Beyond co-writer Doug Jung described the "Ancient Ones" as peaceful: "they weren’t a society that had weaponized anything". [2]
Community content is available under CC-BY-NC unless otherwise noted.