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As a real time strategy game, Grey Goo's gameplay is centered around the movement and management of an army and your base.

The store and lore is centered around Ecosystem 9, which the Beta have fled to after being pursued by "the Silence". The Beta are deeply spiritual, believing everything is written to the designs of a great author - everything, except the Silence.

Having just recently set roots down on the world, the Beta seek to turn on a wormhole generator for their starship, the Suma. The wormhole generator works, but it allows a large invasion force to land planetside.

Believing their old enemy to have returned, the crew at the wormhole generator set the self-destruct to prevent it from falling into enemy hands.

Aran (base commander) Saruk, seeking to stand and fight against the enemy that ravaged his father's generation, rallies his forces to protect his people and understand his enemy...