The monoliths are structures on the surface of Planet that were originally left behind by the Progenitors. A unit can move onto a monolith to gain a morale level. This can only be done once for a unit, so it is advisable to wait until the unit is at Commando before taking the upgrade to Elite. Subsequent uses of a monolith will fully repair the unit if it is damaged. If the unit cannot be healed or upgraded, you will be told "the monolith is silent". Monoliths will eventually disappear if they are used too many times.

Bases can harvest monoliths for a balanced supply of nutrients, minerals, and energy - two units of each. The Manifold Harmonics secret project will increase the output based on your planet rating.

The Ruins is a landmark consisting of eight monoliths in a hollow circle with a lot of xenofungus in the area. This spot allows a player an opportunity to safely hunt mindworms for energy credits, leveling up, and capturing mindworms to add to their military force. Simply move around the fungus, causing mindworms to appear, and then return to the monolith to heal after each battle, thus preventing any risk of losing any units since the mindworms you find will always be weaker than your unit.

Monoliths can also be found as a random result from a supply pod.

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