Aegis of Earth is set 50 years after a deadly event known as the “Silent Apocalypse”. This catastrophic event brought forth various creatures hellbent on destroying humanity. Accompanying the arrival of the creatures was a new element called the "Altenite", which stands as earth's last hope at survival. In the time prior to the game's beginnings, the surviving humans have built fortified cities which have since protected them from various assaults. However, with the approaching “Altered States” and continuous monster attacks, the inhabitants must prepare while continuing to expand and defend their cities.

Players take control of various urban areas, collecting taxes from residents, purchasing equipment, allocating resources and setting up the battlefield with units and artillery to protect the metropolis from the oncoming invasion. Once the battle has begun, waves of enemies will approach, with the player's responsibility being to use the weapons placed in the prior planning stage to defend their city.