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The special-forces unit was the project of the ringleaders, constructed on the BOTTLE SHIP. The special forces was an attempt to create an organization composed of bioforms from different planets to use as bioweapons. The main force of the organization was modeled after the Space Pirates (with actual cybernetically enhanced Zebesians at the center), who had been eradicated from the galaxy with Zebes' destruction.
When Samus herself re-encounters "Dr. Madeline Bergman", actually MB, she is told that the bioweapons went out of control due to a certain presence, which Samus speculated to be the Space Pirate commander Ridley. The real reason was that MB had commanded them to revolt after she went rogue, thus killing all the scientists onboard the station, sans the real Madeline.
Eventually, the project was abandoned in favor of Project Metroid Warriors, an effort to create Unfreezable Metroids for the same purpose and in the same method (by extracting cells and fragments off of the Power Suit.) However, the specimens were kept aboard the station, unexterminated.
It is implied that the special forces unit was composed of many of the BOTTLE SHIP's strongest creatures, namely the Zebesians, Mighty Griptians, Ghalmanians, Asboreans, Super Kihunters and Rhedogians, as all are fought in a long corridor on the way to Phantoon. Because all are spawned from black holes, it is also implied that Phantoon was leading them at one point, because he summons Rage Hands through black holes as well.