Author's Note – A little longer this time, some plot expansion, stuff.

Something I forgot to mention, I said that this would take place between Zero Mission and Metroid Prime, but didn't say when, which would be about 5 months after Zero Mission.

Some of the paragraphs get a little large as well.

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The Galactic Federation

Samus was surrounded on three sides by the Space Pirates on the catwalks above her, the only cover was her damaged gunship behind her at the back of the hangar, too far away to reach. Samus could hear the Pirates' weapons charging, and she readied her arm cannon as well and took aim at one of the Pirates. 'If I'm going to die here, I may as well die fighting.' She thought.

Samus tensed and the Pirates leaned forward as both sides were about to open fire when a commanding voice yelled, "Stand down!" Samus almost shot a Power Beam in surprise as she heard this, then cursed herself for leaving herself open, but saw that the Pirates were also hesitating. She was even more surprised at this, especially since only she should be able to hear a com-link transmission sent to her, when she realized that the voice had come from the hangar's observation deck.

Looking up at the deck, Samus saw what looked like an orange-headed Space Pirate in a strange set of armor that lacked a helmet standing in the center of the observation deck. To the Pirates' right, standing slightly behind him, was another Pirate who wore a gleaming suit of red armor, clearing showing that the armor's wearer was a high-ranking Space Pirate soldier. Even stranger was that the other alien in the helmet-less armor seemed to be very short for a Space Pirate only reaching to just below the red Pirates' chest.

The shorter Pirate yelled again, "I said to stand down! Are you disobeying orders?" Most of the Pirates immediately lowered their weapons, but one of them, standing near the back corner of the left catwalk yelled back at the Pirate in their own language, which Samus' Power Suit translated as, "But sir, it's the Hunter! We should-" The shorter Pirate snarled and cut him off. His voice was harsh and sounded like something scraping together, but he was no longer yelling and Samus couldn't make out what he was saying. As he spoke, the small Pirate raised his arm at the Pirate who talked back at him and balled his claws into a fist, and for a second it looked like his arm grew larger, like he was flexing his muscles.

Samus was once again surprised as the soldier the dwarf Pirate was snarling at began quivering, a sure sign of fear. In Pirate culture, anyone who showed fear was seen as weak, and was usually executed immediately. When the Pirate who seemed to be in charge finished, he turned back to the glass window of the observation deck and said loudly and clearly, "All personnel are to stand down." He then turned to the red-armored Pirate on his right and said, "Captain Gedeon, lower the hangar staircase." The Pirate in red that the short Pirate called Captain Gedeon stepped forward and began pushing buttons on the computer console in front of them. Suddenly, the purple ends on the left catwalk and the piece of metal in the hanger's left side began glowing brighter as large panels of purple metal came out of them, then each panel turned diagonally as they came out, one end pointed down at the floor and the other up at the wall or ceiling. Once in place the purple panels formed two sheets of metal, with the ones from the piece of metal in the side of the hanger forming a ramp from that piece to the hanger floor, and the ones from the catwalk making a ramp from it to the metal in the wall. Then, the middle parts of each panel turned horizontally, forming steps and turning the ramps of metal into a staircase reaching from the floor to the left catwalk. The Pirates on the catwalk faced forward and stepped back against the wall as the small Pirate said, "Samus Aran, I would like to invite you to join me up here."

Curious about this strange Pirate, and seeing no other choice, Samus cautiously walked over to the stairs and up onto the catwalk. As she passed the Pirates lined against the back of the catwalk she turned slightly and kept her hand on her arm cannon, careful not to show any of the Pirates her back. Many of them glared at her as she passed, and the one that talked back to the other Pirate gave her his best death glare, but he didn't have his weapon ready and still seemed shaken up by his superior. 'He must be a very powerful Space Pirate to have this effect on the soldiers.' She thought as she turned the corner of the catwalk and towards the observation deck side door.

As Samus entered the observation deck, she stopped suddenly once she went through the door, staring at the pair of Space Pirates. On Samus' left, just to the smaller Pirate's right and a slightly behind him, was the Pirate in red armor, standing firmly at attention. His body was encased in scarlet armor, with the joints covered by more flexible pieces of black metal. Two fin-like strips of metal ran from the sides of his neck to the tops of his shoulders, and a sea green piece of metal went from the top of his head to down in between his eyes, which burned bright yellow. The skin on his face was deep blue, and two mandibles stuck out of his lower jaw. On the back of his left hand was a gold colored retractable energy scythe, and on his right arm, running from his elbow to his hand was a galvanic accelerator cannon, standard issue Pirate weapons. The cannon was a cold grey color, with gold markings on it and a streak of red on each side, running from the forward points of the cannon to the back end where the cannon touched the elbow. On the left side of the Pirate's chest was a silver insignia, which looked like a leaf with a stem at the bottom and seven points, facing the bottom left and right, straight left and right, upper left and right, and straight up.

The other Pirate that she had thought was short was actually almost completely stooped over, his back hunched at a sharp angle, and his legs looked twisted, his left leg bent out to the side of his body and the right one leaned a little to his right and out in front of him, his foot twisted to the right, causing him to look terribly deformed. The Pirates' face, left uncovered by his suit, was vaguely fish-shaped, with several insect qualities. As the head extended from the neck, it separated, a large ridge coming up from the middle part of the head while the sides dipped down, turned, and connected, forming the lower jaw. The sides of the ridge followed the same shape, forming the upper jaw. The ridge curved inwards from the sides, making the center of the ridge stand even higher. The Pirates' jaws were orange, the sides of the ridge that started the upper jaw was a faint yellow, the central ridge was grey, and the top of his head and neck were a faded red. His head was wrinkled, and his upper lip looked thin and the skin on it seemed cracked, making it look like his skin was stretched, barely able to cover his head, but his mouth shined with rows of long, white, needle-like teeth, which looked both sharp and well cared-for. Two transparent tubes ran from somewhere on his upper back and up the Pirate's neck to his face, where it curled around the sides of his mouth and inside, where they rested between the teeth on his lower jaw. These tubes were filled with what seemed to be a dark green gas. His strangest aspect, though, were his hands. Space Pirate hands were similar in size and shape to Human hands, but they only had a thumb, a pointer finger, and next to their pointer finger was a large, thick hook-like finger. This Pirates' hands, however, were also extremely large, over twice the size of Samus' own hands, making them seem grossly out of proportion to the rest of his body.

Samus also looked at the Pirate's power armor. It covered all of his body except his head and the top of his neck in metal. The arms, legs, and parts of the chest and waist were covered in a flexible purple metal mesh, while most of his chest and waist, as well as his hands and feet were in a hard bluish-green shell of metal. The armor didn't seem to have a visible helmet.

"Samus Aran," the strange Pirate said in a firm, confident voice that sounded faintly raspy, "welcome to Vortex Outpost. I am Doctor Conleth, the head of this facility, and this, "he said, gesturing to the Pirate in red on his right, "is my head of security and bodyguard, Captain Gedeon."

Samus was already suspicious. 'Why did he stop those soldiers and call me here? Does he think this one Pirate will be able to protect him? And just what does he have planned?' Samus decided to find out just what he wanted from her. "Why did you call off your soldiers?"

"Why wouldn't I?" Dr. Conleth said in an irritated tone. "Fighting with you is pointless, and I'm not just saying that because you could kill them easily. The way I see it, you are not our enemy." He paused then said with conviction, "The Galactic Federation is."

Now Samus was intrigued. "I'm not your enemy?" she said in a disbelieving voice. "Even after the Assault on Zebes?"

Conleth growled at this. "True, you have done us severe damage in the past, destroying our forces, our bases, and our research. But you did us some favors during the Assault on Zebes, and from what I hear the Galactic Federation has decided you're an enemy of theirs as well."

Samus wondered at this. What could she have done on Zebes that helped them? And what was that about the Federation? "What do you know about the Federation, and what do you mean, I did you a favor?"

Dr. Conleth gave out a hissing chuckle, and his mouth widened into a smirk, showing his pointed teeth. He said in an amused voice, "When you destroyed our forces at Zebes, you also destroyed what remained of High Command. You see, when Mother Brain defected from the Chozo and took over our organization, she designated the Chozo Grey Voice as troop leader, Ridley as general and war strategist, and herself as planner and supreme leader." Samus eyes narrowed and she clenched her fist at hearing Ridley's name, but Conleth continued on. "Grey Voice betrayed Mother Brain and attempted to destroy her, though he failed and that savage Ridley killed him. Afterwards, you killed both Ridley and Mother Brain, forcing us to create a new High Command. While some Pirates complain about the setbacks, I am not completely unhappy with the change in leadership." Dr. Conleth took in a deep breath, sucking the dark green gases flowing through the tubes into his mouth faster. "As for the Galactic Federation, our scanning equipment picked up your little skirmish with their forces. Besides, you didn't really think they'd let you keep that Power Armor, did you?"

Samus was beginning to get frustrated. Every answer created another question! Still, she needed to know what the Galactic Federation was up to. She answered cautiously, "And why wouldn't they allow my armor?"

"Why wouldn't they?" The Pirate's tone was mocking her. "Why wouldn't they allow you to keep a powerful piece of Chozo technology? Technology that was used to help win a significant amount of otherwise hopeless battles, including the Assault on Zebes, which even the Galactic Federation's immense naval might couldn't win?" Dr. Conleth looked directly at her and said seriously, "The answer is simple. They believe that, with your Chozo armorsuit, you are the equivalent of a super soldier. Federation scientists will no doubt already have tried replicating your suit's advanced abilities. However, I have already studied the Chozo's bio-metal technology, as I am the Space Pirate Confederacy's peerless bioresearch scientist, and I can say with certainty that creating a working copy of the Chozo Power Armor is practically impossible." Dr. Conleth spoke with clear confidence and pride. "Since they couldn't reproduce and manufacture Chozo Power Armor for their own marines, they decided to simply use you to attack us for as long as they could. Things changed, however, when you finished the Assault on Zebes. Our forces scattered, the bases destroyed, our research and experiments lost, and our entire leadership killed, the Galactic Federation doubtlessly no longer considers Space Pirate forces an adequate threat. Since they no longer need you to keep us in check, they can move on to the next best thing for their super soldier research; taking your suit and studying it in their own laboratories, and field testing it and the resulting prototypes with select marines."

Samus stared at him in horror. It all made sense. With the Space Pirates out of the way, they didn't need her, and could try and take her technology for their own purposes. Samus thought about the captain of the G.F.S. Enyalius remark about her loyalty to the Federation. 'Wait' she thought. 'This is just a conspiracy theory to turn me against the Federation.' Samus' tone was harsh. "You're lying." She said, pointing her arm cannon at the Pirate. "The Federation isn't that corrupt."

Samus saw movement to the side and pointed her cannon at the other Pirate, Captain Gedeon, who was now aiming his own weapon at her. He stayed so still, she had almost forgotten he was there!

Dr. Conleth put his giant hand up. "Violence will not be necessary." He said to Gedeon, and then turned back to Samus. "And you are wrong if you believe that the Galactic Federation is not corrupt, Samus Aran. Many events in the past follow specific patterns, and by watching history, we can learn when these patterns appear, what they affect, and how they work. For example, one pattern that can be seen in history is the downfall of civilizations. After so many years of existence, many civilizations have what is called a 'golden age', a time of peace and prosperity where everything is easy and abundant." The doctor's voice became grave. "Eventually, however, this golden age must end, and few, if any, of these civilizations get to experience another golden age. The end of these peaceful times is often marked by some terrible event, such as a fresh chain of disasters or a series of battles signaling the beginning of a war, causing things to become more expensive and less abundant. Fearing the end of their prosperity, people begin to hoard the commodities around them, whether that is money, food, or power. Governments, too, try to resist the end of their wealth, and begin trying to increase their own strength and power to survive the coming ages. Eventually they begin to ignore and overstep their own laws, little things at first, which grow bigger with the years. More extreme forms of corruption, such as illegal experimentation, soon follow."

Dr. Conleth paused before continuing his speech. "These governments and those pulling the strings of course try to keep the growing corruption out of the public eye, but eventually deception of so large a scale must be revealed. After that, things begin to worsen, until the people of that civilization decide that they have had enough and turn against the corrupted government, which in turn sends its' soldiers against the rebelling people in a bloody civil war. This event usually ends in one of three possible outcomes."

"The first outcome is for the ruling government and its' soldiers to defeat the rebel forces, in which it would be reformed with additional laws to protect against the event happening again, and the old government slowly rebuilt."

"The second outcome, of course, is for the rebel forces to topple the government, and then the leaders of the rebellion create a new ruling body of government in the people's interests with themselves as its' leadership."

"The third, and by far the worse outcome, is for both sides to decimate the other, leaving what few survivors remain to pick up, and either work together or apart to create new civilizations."

Samus was silent. 'His theory is well-made, but even if that's true, what does it have to do with the Galactic Federation?'

Dr. Conleth took another deep breath before continuing. "Now, all you need to do is take the pattern, and apply it to our current situation; the one with the Galactic Federation. You see, the Federation has already had what it considered a 'golden age', which ended with the beginning of the more serious Space Pirate raids. Most notably, the K2-L raid."

Samus glared fiercely at Conleth when he mentioned K2-L. She was born on that colony, and had only been three years old when the raid happened. Her father sacrificed himself to deprive the Pirates of the supplies they had come to steal, and her mother died protecting her from Ridley. She was – and is – the colony's only survivor.

Conleth paused a moment, then continued. "The Galactic Federation's golden age ended about seventeen solar years ago. Because of our forces pressuring them, the Federation has had little else to do but focus on finding ways to fight us, which they could barely do without asking for the help of Bounty Hunters. Now that we are not currently considered a threat to them, the officials of the Galactic Federation will be able to focus on other things, and considering their poor defenses during their war with our Confederacy, their main concern will probably be to strengthen and arm themselves for a new enemy or for the eventual return of our forces. The most obvious way, and possibly best way to do this, is to secure and study your Power Armor." Conleth exhaled loudly. "And then there's the whole 'gathering corruption' thing to deal with, so obviously the step after that is illegal experimentation – if they're not already doing that with the data they already have. Once their super soldier program and whatever else illegal things they've done becomes common knowledge, the public will rise up, and the Galactic Federation will have a civil war on its' hands, and considering that the Federation will have an army of marines and a smaller army of super soldiers and the rebels will be everyone else in the Federation, well I'm sure you can figure it out."

The doctor prepared himself for the next part. "There is, however, an alternative."

Samus studied him carefully. She didn't like where this was going, but if this Pirate was right, she would need to do something about the Federation – for herself and for the Federation's innocent civilians. "What alternative is that?"

Conleth's eyes gleamed as he spoke. "If one civilization defeats another, and its' leaders decide to annex the other civilization, then the conquered are merged with the victor, and the two governments and cultures become one. During the ages ahead, the single new civilization adapts to the changes of adding one to the other, the culture blending and the government being cleaned, refined, and reformed. This sweeps away much corruption and dissatisfaction for many years, allowing the new civilization to live longer, eventually experiencing a new golden age before it begins to decline again. This, too, has been revealed to me by studying the past. Take, for example, a rather old civilization, which existed on the old Human homeworld, Earth." Samus' eyes widened at the mention of the planet. While she had been born on K2-L, she knew that her parents had come from Earth to help build the colony. "This civilization, which was called Rome, conquered many other countries, adding them to it, allowing the civilization of Rome to be reborn twice, and letting it exist for over 2,000 of the planet's years."

Samus had heard enough to guess what the doctor was getting at. "So, you're saying that if your Confederacy defeats the Galactic Federation, you'll both survive longer."

"Essentially, yes. With their overconfidence of our defeat, we could defeat them." Dr. Conleth paused. "With your help, that is."

Samus was taken aback by this comment. 'Is he asking me to join the Space Pirates?' She didn't know if she should be surprised or angry. She decided on angry. "You want me to help you defeat the Federation? After all you've done to me and the innocent people of the Galactic Federation!"

"Ridley, not I." Conleth answered simply.

"What?"

"Ridley, the Space Pirate leader at the time, was the one who ordered the attack on K2-L and killed the colonists. He was also responsible for all other Space Pirate raids before we finally took Zebes."

Samus knew he was right. But the Pirates had still played a large role in things, and they did many terrible things against the people of the Galactic Federation. "But it was the Space Pirates who wiped out the Chozo colony on Zebes, and your scientists who tried using the metroids as bioweapons!"

Both of the Pirates looked irritated at the mention of the metroids.

"That," Dr. Conleth began in a cold voice, "was Mother Brain's doing. After repeated failed attempts of taking Zebes, she decided we could be useful to her, and she lowered the shields around Zebes and allowed us to attack. After the battle, she declared herself the planner and head of the Pirates, the Chozo Grey Voice as troop leader, and Ridley as the general and military strategist." Then he said with interest, "A position that I hear was first offered to you."

Samus stared at him hard. "And I rejected it immediately. I could never work with her after she helped you Pirates, and for what she did while I was still living on Zebes."

Conleth nodded. "I realize that. And I ask you to reconsider. Before you decline, hear me out." He said, cutting her off. "Both Ridley and Mother Brain, thanks to you, are dead. And as I told you earlier, a new High Command has been made to replace them, and our Confederacy still plans on defeating the Federation. However, are forces are still rather crushed, and in disarray. Additionally, it will take time before the new High Command will be able to work efficiently. At the moment, we are at a significant disadvantage to the Galactic Federation, especially now that they're actively trying to replicate your Power Armor. In order to quickly come back from the situation, we need a great mind to lead us into battle against the Federation in order to harm them and return their focus to us. The Galactic Federation is now hunting you, we need a leader, and your reasons for fighting us are rather dead now, so I ask you to reconsider the offer and become our new leader." Dr. Conleth cleared his throat. "Of course, I'm not asking you to decide on it now. I see that your ship has sustained quite a bit of damage from your earlier… encounter. Powering the life support functions for a full rest cycle while attempting to repair the ship's damaged parts will slow the process, so, if you would like, we have unused rooms for high-ranking personnel."

Samus thought on this. There was something suspicious about the whole thing. Still, this would help her find out just what was going on with both the Space Pirates and the Galactic Federation. And it would take some time for the ship to auto-repair the engines…

"Fine, I'll think on it." She said in a controlled voice. "In the meantime, about that room."

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Author's Note – A little note for the character descriptions here, Captain Gedeon is based off of the Pirates of the first Metroid Prime, while Dr. Conleth is supposed to look like a malformed Pirate from Metroid Prime 3: Corruption.

Also, 5 points to anyone who can guess what the insignia on Captain Gedeon's armor means without looking it up. I'll post the answer next chapter.