AIM2 Clan Wars tells about new events that take place in the Polygon universe. When Super's control ceased completely, a great opportunity presented itself for the mechanoids to gain access to undiscovered areas. After the Reformation process, the characters changed dramatically, many ancient clans sank into oblivion, and their simple and primitive goals disappeared forever.

New factions with mechanical heroes of the 5th generation at their head have become strong and invincible military formations that have clear goals and a strategy proven in many deadly battles. Finding himself in such conditions, the user of the game Mechanoids 2: War of Clans will plunge headlong into a cruel and irreconcilable world in which wars are no longer fought for imaginary superiority over others, but for the sake of the all-encompassing and total annihilation of all rivals. Those who were able to subjugate resource extraction in time took the path of an economic war that dragged on for years.

Now the Counters decided that they needed to summon a great hero who could bring back the first ruler of the rebel tribes, who had disappeared in an unknown direction. This will help restore the usual course of things and subdue the uncontrollable rebels, who began to possess not only power, but also secret knowledge. The leader of one of the losing clans goes on a search, but with the condition of restoring his former position and power. Whether such an important mission will be completed now depends only on the player.