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Cooperative missions are unique story-driven missions that take place during the events of the main single player campaign. These missions often are stand-alone missions, providing additional context to the greater war, or the missions explain and elaborate on events that occur within the single player campaign. The missions are usually, but not always, harder than normal due to the presence of two human players.

A few missions with simple objectives (such as Thunder God and Neuromancers) makes it possible for solo play with an A.I. ally. To do this, select the LAN option in the main menu, create a game, select the right cooperative mission then choose an AI difficulty like in Skirmish (Hard AI being the most reliable ally out of the 3).