The physical and non-corporeal Koinonians coexisted on the planet, however, the physical Koinonians destroyed their own civilization in a series of bitter conflicts between different factions. They lasted for generations, centuries before the 24th century. Those conflicts were later called the Koinonian Wars. They left ruins in underground caverns and only sparse data about the corporeal Koinonians survived into the 24th century. The non-corporeal Koinonians had strong morals and watched the raging wars in abhorrence. They survived on the homeworld even after it was ravaged by the wars and still inhabited the desolate planet in the 24th century. They considered the wars a tragic but dishonorable past and didn't tolerate any more suffering on their homeworld.
In 2366, the USS Enterprise-D studied the remains of the civilization. Markings in those caverns and subterranean tunnels were identified as Koinonian thereby making the identification of the planet as their homeworld possible. One room discovered was a large ceremonial chamber, but it was trapped by the Koinonians using explosive devices with subspace proximity detonators, remnants from the Koinonian Wars.
One of these devices exploded and killed Marla Aster because it wasn't detected. The Koinonians, out of guilt, dug up the other bombs and disarmed them. Furthermore, having sensed the pain of Jeremy Aster, now an orphan, they decided to bring him to the planet to take care of him. Tapping into the antimatter from the antimatter pods of the Enterprise, they created a replica of his mother and old home on Earth in order to convince Jeremy to come there. After the interjection of the Enterprise crew, they later accepted that Jeremy was in better hands with other Humans and the Marla Aster replica ceased to exist. (TNG: "The Bonding")