Their primary purpose is detecting cloaked and subterranean units and buildings as well as approaching enemy units. In order to be used the MSA has to be deployed. This was necessary because the highly sensitive microphones and scanner arrays are otherwise distracted by the vehicles' own vibration and motor noise.
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.