Galactic Federation Council

The Super Metroid manual relates the events that immediately preceded Metroid II thusly:


 * After the skirmish on Zebes, a special corps was assigned by the Galactic Federation to destroy the Metroids on SR388. That corps was never heard from again. The Supreme Council gave Samus the job to fly to SR388 and do what the special corps could not do--make the Metroids extinct.

Because Samus was ordered to SR388 by the Galactic Federation, we can assume from this information that the Supreme Council is the ruling body of the Federation.

The members of the Council are unknown. Presumably, some or most are human, as most of the members of the Federation seem to in other Metroid games. It is possible, however, that individuals of other species may also be members.

It is also possible that the Supreme Council involves one or more Aurora Units. We know from Metroid Prime 3: Corruption that Aurora Units have been in use 20 years prior to the events of that game. The Prime series takes place after the original Metroid storyline, and therefore before Metroid II. Therefore, Aurora Units could very well be in even more widespread use during Metroid II.

Alternatively, the events of Metroid Prime 3 may have made the Federation wary of using Aurora Units.

This information is mostly speculative. The specific nature of the Federation's ruling body is as of yet unknown.