The Soul is an enemy that appears in the Northern Ruins in 600 AD in 1000 AD. This enemy, along with Fallen and Flesh Reaper, can be encountered in the present if they are not killed in the past. You can fight them again in the past even after killing them in the present. But, they cannot be encounter vice versa.
Note: If a Soul is with a Fallen, the Soul will posses the Fallen and merge to become a Fallen + Soul.