The Galactic Federation communications array is only seen in Metroid Prime 2: Echoes. Existing in the Communication Area of the Temple Grounds, the atmosphere of Aether in its current state renders it useless, jamming the signal. Samus Aran discovers this when she tried to scan an Interface Module. It can be assumed that the Galactic Federation took it back with them when they visited Aether.
"Object scan complete. Target identified. Galactic Federation communications array. Target is part of a deep-space communication system. Local interference is jamming its signal. Until conditions clear, it is effectively useless."