Galactic Federation (Metroid)

The Galactic Federation are considerably antagonists in the Metroid series. While not open villains, their darker side is revealed more and more as the games progress; by the Metroid Prime trilogy they seem to be on par with the Pirates in their goals. They will not hesitate to use terrorism, in one point they even turn Samus into a human bioweapon by injecting Phazon into her.

Early signs of corruption
The first sign of corruption in the Federation was seen in Metroid Prime 2 Echoes, when they experimented with Phazon, despite its destructive qualities. When they left planet Aether they took large amounts of Phazon with them, for bioweaponry purposes, and they set about developing the Phazon Enhancement Device. One of these was later given to Samus turning her into a living weapon.

Mid-corruption
In Metroid Prime 3 Corruption, the Federation were giving full Phazon devices to their soldiers, even causing them to suffer Phazon sickness - one soldier is seen shaking his arm, but brushes it off eventually. The Federation are also revealed to have a shadowy overseer who gives orders. He is never seen, but his goal of using Phazon against the Pirates seems questionable.

Full corruption
In the events of Metroid: Other M the Federation were using full biological experiments to make an army of Zebesian Space Pirates; their original enemy, they had cloned them and also cloned Mother Brain herself, and were planning on amassing an army. Samus and Adam Malkovich found this out and planned to destroy the research. Adam blew up the station and Samus destroyed the bosses which the Federation had  cloned; thus severely angering the Galactic Federation.

Future
Despite Samus being trained by the Federation, it is unknown what will happen in future games. Presumably the Federation, with their dark side revealed, will be antagonists, as Samus went into hiding from them in Other M.