Scrin Motherships are equipped with an artificial intelligence that served as a command and control interface, but was far more sophisticated than an EVA. The Mothership was capable of performing a number of functions, including monitoring and analysis. It was even capable of questioning and even disobeying orders, similar to CABAL, since both were made out of advanced alien technology and had minds of their own. Unlike CABAL who cared about nothing but its own goals, the Mothership AI actually showed concern for its superior's (being Foreman 371) well being, even going so far as to disobey the orders of the higher-ranking Supervisor. Like other interfaces, the Mothership was able to communicate, speaking with the Scrin's equivalent of a female's voice.
During the Third Tiberium War, the Mothership awoke the Scrin mining fleet under Foreman 371. When it realized that the human population was still capable of resistance, the AI recommended that 371 abandons the mission. However, the Supervisor ordered the operations to continue.
During the conflict, the Mothership continued to assist the Foreman while still urging that the mission be aborted because of the formidable native resistance.
The Supervisor ordered Foreman 371 to seek out more information about Kane, a goal which superseded harvesting in its importance. After 371 successfully captured two data hubs which confirmed the Overlord's suspicions that the liquid Tiberium explosion had been intentionally caused by Kane, the Supervisor ordered further investigation. However, the Mothership alerted the Foreman that the humans were attacking the Threshold tower assemblies, which were 371's only way to leave Earth. The AI urgently suggested to 371 that it complete at least one tower, putting aside all other objectives. The Supervisor told the Foreman to reformat the Mothership, which replied that the Foreman would be stranded on the planet and die without Tiberium infusion. The Supervisor angrily stated that the harvesting expedition was expendable, and that the Overlord demanded more information about Kane. The Mothership promptly induced a "communication failure", cutting off contact with the Supervisor and dismissing its command. It went on to brief Foreman 371 on the construction of Threshold 19.
After the tower was completed, the Foreman defended it against GDI assaults, the Mothership was summoned and escorted to the Threshold, where it prepared to transport 371 through the portal to the Ichor Hub. With both entities saved, the Mothership congratulated the Foreman on salvaging the mission.