The upper atmosphere of SR-388 in Metroid 2 hurts Samus. This is because, prior to the start of the game, the planet had been glassed with nuclear weapons by the Galactic Federation. Samus's mission was therefore to exterminate the last enclave of Metroids that survived by being underground. The Federation would have glassed the planet earlier, but until the aftermath of the Prime series there was not enough political will to get the necessary supermajority of the senate to approve this drastic action.
Additionally, Biologic Space Labs was a biotech company contracted by the GF to preserving the wildlife of the planet prior to its nuclear holocaust. Samus's visit to SR-388 in the prologue of Fusion was the result of her being hired in an advisory capacity to oversee the repopulation of the planet, owing to her familiarity with its natural wildlife. Moreover, BSL was already secretly aware of the X parasites, which is why they were able to so quickly conjure up a working vaccine when Samus was infected. Any zombies or infected persons on the station happened to have received a placebo in their ongoing clinical trials (while everyone else was simply underequipped).
Also (mostly unrelated) Federation Force was an in universe recruitment tool, similar to the game America's Army.