In PoE patch 3.1, War for the Atlas random maps on your Atlas could gain Shaper Influence (S-I) or Elder Influence (E-I). On the Atlas, maps with star clouds have S-I and maps encompassed by the grey blob have E-I. Elder influence will only start appearing after you have ran your first S-I map that is Tier 6 or higher. Unique maps cannot have S-I/E-I. Note, having enough path of exile orbs in game is not bad for you.
Effects of Shaper Influence – In a S-I map you may encounter extra mobs, have frost balls follow you which form Vortex ground on contact or have the boss enhanced by the Shaper with Cold based abilities. Sometimes Agents of the Void will spawn after killing the map boss. Rare Shaper items also have a chance of dropping.
Effects of Elder Influence – In an E-I map there are always bonus mobs. These can be several Null Portals which continually spawn mobs until the portal is defeated or tentacle, octopus mobs that fire projectiles. In some maps tentacles may appear from the ground slamming your character. Rare Elder items also have a chance of dropping.
Spreading Elder Influence – Completing a S-I map that is adjacent on the Atlas to an E-I map will change that map to become Elder influenced. Conversely completing an E-I map will remove the E-I and may replace it with either S-I or no influence. When you have approximately 19-20 E-I maps the Elder and his four Guardians will occupy five E-I maps (effectively random which ones are occupied. Note E-I/S-I can change randomly on your Atlas when running maps with no influence.
The Elder and his Guardians – You must defeat the four Guardians before you can face the Elder. A Guardian occupied map replaces the normal boss. Once you defeat the occupying Guardian the E-I will disappear from that map. Once all four Guardians are defeated you can take on the Elder. Once the Elder is defeated all E-I is removed from the Atlas (there should now be much more S-I on the Atlas). Running S-I maps will cause the E-I to eventually return. Note that maps occupied by the Guardians/Elder are permanently influenced until the boss is killed.