Mother Brain was a creation by the Galactic Federation and Samus is just informed about this. Mother Brain was created to learn about communication techniques and weaknesses of different creatures in different planets and the home of Mother brain was planet Zebes.

The project was called Okazuno…Roughly translated to Mother Brain. Mother Brain then decided that she didn't need to be doing this and started to take over the planet and control it. And this is where the Metroid saga begun. The federation found that mother brain was corrupt and was doing things they programmed it not to do so they sent Samus to destroy the brain. The federation thought they found what was wrong with their program and sent another mother brain out to Zebes, but this time it became even stronger and mutated. They once again sent Samus to destroy mother brain, but at the same time, destroy the entire planet. This is now where the story begins. Samus can't believe that the federation would do such a thing and is extremely mad at them for putting her at risk of death just to clean up their problems. She is then informed about Project Otazuno…Father Brain. She gets even more furious because she knows she's got to do something about it. She is then introduced to another space hunter who was hired to help Samus.  While the Federation is preparing for attack on the planet, Father Brain is doing planning of his own.  He creates a new Mother Brain, one that is perfect in every way, yet a complete menace to the Galactic Federation. He then creates Kraid, Ridley, and some new menaces.  He reshapes the world to look much like what Zebes once looked like. How he knows what Zebes looked like is a complete mystery. It is Samus's job to destroy it all. Father brain then realizes that since he is a failure to the federation he has to do something to make sure his death isn't possible and then makes himself and Okazuno into the planet…The two space hunters take off to the new Zebes...and this is the start of Metoid : Project Otazuno...

We will have more about weapons and things like that later...

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