You arrive just outside of Phaaze, the armada is attacked by these Pirates that have taken Dark Samus as their leader. The fleet takes care of them while you go ahead, you have more important things to do.

Land and you're immediately overwhelmed by the amount of phazon entering your body. So much so that your energy tanks are on emergency cooldown and you're stuck in hyper form. Your own ship doesn't recognize you so unless you cool off and get rid of this phazon, good luck getting home. Almost like a version of Arkham City. You're given a bar, this is a reverse health bar, if you don't expend your phazon and the bar reaches max then you die. You're in her territory now. If she decides to overload you, it's game over. She controls the game, you are like her. In fact, when you do die, you literally become her. You fall down a hole. A hole into Wonderland. At the bottom, Metroid eggs. You keep going deeper, making your descent as weirder and worse things come your way until you reach Dark Samus herself, practically the Queen of this planet, I mean she's the remains of Metroid Prime. You take her in battle, new abilities, some from the very Hunters you were once friends with and had to destroy. But she seems like an easy fight. She steps back and let's Aurora 313 rise out of the ground, absorbing Dark Samus. That's right, the AI from the Valhalla ship, calling way back to Mother Brain of the first game. You destroy the unit, glittering back into the form of Dark Samus, only for her to disappear. Along with her...Samus's phazon capabilities, she's clean. Her blue glow is now gone, she can go but it may be too late, the planet itself has lost its power source, therefore explodes. The fleet escapes, this time without the Leviathan they used to get there. The commander asks where Samus is, the cadet replies that the crisis is over but no contact from Samus. Just then her ship passes by, sending a transmission. That transmission: "Mission Complete." What an utter boss.