Their primary purpose was detecting cloaked and subterranean units and buildings as well as approaching enemy units. In order to be used the MSA had to be deployed. This was necessary because the highly sensitive microphones and scanner arrays were otherwise distracted by the vehicles' own vibration and motor noise.
GDI commanders used these units for early detection of incoming Nod surprise attacks, and for assaults on cloaked bases. Similarly, Nod commanders mostly used the MSAs against enemy Nod commanders, especially during the Nod Civil War. In addition, Limpet Drones could be uncovered and destroyed to prevent infiltration.
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The Mobile Sensor Array requires to be deployed in order for it to detect incoming enemy units. It can detect cloaked or subterranean Nod units. Since Nod has monopoly on the two aforementioned technologies, GDI forces were the only ones that actually deployed them in the Campaign. However in skirmish/multiplayer matches, the MSA is readily available to any GDI or Nod commander.