"First of all," said Ashen Feather, "what is the current condition of the Space Pirates? The bad ones, I mean," he added quickly.

Odius contemplated this for a moment. "Not very good. Since the SA-X was freed, nothing seems to have been working to their benefit. Their troops have already been split into three factions: ourselves, the pirates remaining loyal to High Command, and the pirates that succumbed to the X. Only the last one seems to be in any good condition."

Ashen Feather nodded thoughtfully. "Then the Galactic Federation should be our main concern. They're the most direct threat to us at the moment…well, aside from the X, of course, but killing them all off isn't very feasible at the moment. We should probably -"

"The Metroids," Samus gasped suddenly. Ashen Feather blinked. "What?"

"I had almost forgotten…the Federation still probably has a Metroid breeding facility somewhere out there. If we could get a hold of a sizeable amount of Metroids, then we could set them loose on the X and end that threat just like that!"

Ashen Feather frowned. "That's great and all, Samus, but we don't know where -"

"Lycas," Samus replied promptly. "I was planning to head to that planet before I got entangled in this mess. It's a cold planet on the fringes of Federation space; ideal for storing Metroids while maintaining a low profile. Plus, there's a Federation vessel stationed there, so the planet must have something of importance."

Odius glanced at Samus skeptically. "Are you sure about this? It sounds to me like you're basing this plan on instinct alone."

Samus smirked. "It was instinct that got me through all those experiences you mentioned, as well," she retorted.

-=-=-

"Mr. President, sir?"

Rodriguez glanced up, his hand quickly disappearing from view. A nervous-looking man was at his door – a scientist, based on his uniform.

"Come in," he greeted the man. "What can I do for you?"

The man shuffled in tentatively. "Well, sir, I'm one of the workers assigned to the X project…"

At this, Rodriguez listened in closely. "And? Have you made progress?"

He nodded. "We have, sir. We've discovered an X-repellant that can be used on Federation uniforms to prevent infection from the parasite. We may now begin more intensive study of the organisms…is there any particular subject area you want us to research?"

Rodriguez assessed his threats for a moment. Aran, of course, came to the forefront of his mind…the X had been a fake, of course, so the real one was probably still out there somewhere…

"Two things," he said. "First, I want you to find a way for us to take control of the X, so that they won't turn on us. Second…I want you to find a way to remove their weakness to Metroids. Got that?"

The scientist nodded. "Of course, sir." He backed out of the office and left.

Now that he was alone once again, Rodriguez went back to studying his hand.

His translucent, sickly green, clawed hand…

-=-=-

"Careful, now," Odius whispered. "The X hadn't found this place when I last checked, but things could have changed. Samus, you take point."

The bounty huntress nodded and moved ahead of the others. Even she had never discovered this exit to Crateria in her prior visits to Zebes…it only reinforced what she had known all along: that almost every world she visited was an enormous, confusing maze that she could never hope to fully explore.

She walked out into the light, swiveling her arm cannon back and forth in search of threats. There was no sign of any, but you never knew.

"Our ship should be just beyond those trees," Odius murmured.

Samus nodded and started forward, eyes ever-watchful.

Clank.

Her ears pricked up as she heard the distinct sound of metal. Someone else was there…

Clank.

There it was again.

She signaled for everyone to stop, and her eyes scanned the surrounding area. She couldn't see any sign of –

There!

A brief flash of yellow, orange, and red in the trees, and Samus knew what she was up against: another SA-X.

Did it know that they were there, though?

Samus remained frozen in place for a minute, giving the SA-X enough time to get away from them. At last, she started forward again.

As she walked through the trees, though, she began to sense that something was odd. No sounds followed her…shouldn't the others at least have been making some sort of noise?

Finally, she had the sense to turn around. The others weren't there.

"You've got to be kidding me," Samus groaned as she turned back in search of them.

-=-=-

Wesley, White Voice, Ashen Feather, Odius, and the rest of the Space Pirate renegades waited with bated breaths as Samus walked forward. They were to follow once Samus had reached the trees…

Suddenly, she stopped. The others glanced at one another, as if to ask why.

Then, she simply disappeared.

Their eyes widened in surprise, and they took this as a sign that they weren't safe. They turned to leave…but there was Samus again, right there behind them.

"What -" Ashen Feather began, but Samus placed a finger to her lips and beckoned for them to follow her. She turned and walked back into the caves, and the rest followed.

Wesley frowned, though. Something seemed off about this…


"Have you heard?"

"About the president?"

"He's gotten so weird since the incident earlier…"

"And why is he wearing that glove now?"

Whispers and furtive glances followed Galactic Federation President Martin Rodriguez as he walked through the corridors of the Federation capital. They couldn't be helped; what with all the strange occurrences lately, rumors were bound to fly around. He could try to dispel some of them, but they would only be replaced by new ones. Better just not to address them.

He flexed his hand again, marveling at the way the claw bent and stretched in ways the human hand could never do. He was fascinated by this transformation, and, more importantly, eager to learn what sorts of powers it gave him. That would have to wait, though.

Because right now, he had three very important visitors arriving. He glared down the hallway as he thought about them, hatred boiling up inside of him.

Oh, yes. Three very important visitors indeed…

-=-=-

"Samus…I don't think heading this way is a good idea," Ashen Feather pointed out as they headed deeper into the caves. "We're going to run into a group of X, and if that happens, you'd be hard-pressed to defend all of us."

The bounty huntress didn't respond.

"We should probably go back," Odius agreed. "Whatever you led us away from out there can't be that bad, and we at least have a chance of escape."

Wesley nodded faintly, the wheels in his head turning as he struggled to figure out what was wrong. Samus wasn't talking, of course, that was one thing, but there was something else…

Clank, clank, clank…

The distant noise of footsteps interrupted his train of thought. Metal footsteps…then they were one of the Samus clones!

"SA-X!" Odius gasped. "One of them's found us!"

"We'll back you up, Samus," Ashen Feather said. "You've held your own against one before; you can do it again, I'm sure."

Samus nodded silently, and Wesley began to piece everything together.

-=-=-

Voices echoed down the corridors of Zebes. They couldn't be too far now.

Samus checked her condition. Everything seemed to be in decent shape…she could probably save her allies without too much trouble. With any luck, they would help her out, as well…

As she rounded the corner, all of them came into sight. "There -" she began before being forced to duck out of the way of about eight shots.

What were they doing?!

She instantly fired off a charged shot at the SA-X before the rest of her allies – enemies – whatever resumed fire on her again. Samus rolled up into morph ball mode and rolled between their legs, dropping a few bombs in the process. The bombs wouldn't injure them; just knock them off-balance, that was all…

The SA-X had been content to hang back until there was a direct threat to it, but now it moved at a surprising speed, striking Samus with an Ice Beam. The bounty huntress unrolled and fired off an Ice Missile in response. Several more shots whizzed by her from her allies at the same time…well above her shoulders. Did they really have such terrible aim?

"Samus!" Wesley gasped suddenly, seeing the Ice Missile. Samus rolled her eyes. Great. Now he could see the obvious?

Samus continued her assault on the SA-X as the rest of them, sans Wesley, aimed at her. "Stop, stop, stop!" Wesley shouted, getting in front of their weapons. "We've been tricked! It's Samus!"

"What are you talking about, you idiot?" Odius asked. "That's the SA-X. Can't you tell by its oversized shoulders?"

What the…I don't have oversized shoulders anymore, Samus thought in surprise. She leapt to the side, avoiding a missile from the SA-X.

"We're being tricked!" Wesley repeated. "The SA-X doesn't have -"

"Out of the way," Odius snapped, pushing Wesley off to one side. "You're going to get us killed at this rate."

Wesley turned to Ashen Feather and White Voice. "Won't you listen?" he asked.

"Make it quick," Ashen Feather said grimly. "We don't want to stand around for long."

Meanwhile, Odius and his half-dozen troops came to the SA-X's aid, firing off their energy pistols at Samus. The clone nodded in satisfaction.

Samus did her best to dodge them, but a few still singed her armorsuit. She gritted her teeth in annoyance. This was not going to be enjoyable…

"It used the Ice Missile," Wesley pointed out.

"And your point is…?" Ashen Feather asked.

"Only Samus has the Ice Missile," argued the former Federation trooper. "It has to be her!"

"The SA-X easily could've copied it," replied Ashen Feather.

"But the one we think is Samus is still using the normal missile! She wouldn't stop using the Ice Missile for no reason!"

Ashen Feather sighed. "Fine. But that doesn't explain why what you're claiming to be the SA-X has Samus' Fusion Suit and why Samus has the original Varia Suit."

Wesley had no answer to that.

Samus went back into morph ball mode, having no choice but to unload her most powerful attacks. She planted a Power Bomb in the SA-X's vicinity and sped away, praying that Odius and his troops would have the sense to get out of the way of the blast.

They did, but they were also still unaware that she was the real Samus…so as she rolled through them, one of them managed to stop her and fired upon her.

Samus unrolled and stumbled back, frantically trying to escape from the stinging energy bullets. Behind her, the Power Bomb went off, and suddenly, Odius pushed her back into the blast radius of the miniature nuclear weapon.

Her eyes widened, and she let out a bloodcurdling scream as her entire body was wracked with pain. She maintained just enough focus, however, to fire off her grapple beam at the SA-X and drag it into the blast, as well…

The illusion faded as both Samus and the SA-X fell to the ground, seemingly trading positions. Their armor was cracked and shattered in some places A viscous yellow fluid bubbled up from the SA-X's form.

"Wha…" Odius began. "What just happened?"

Ashen Feather's eyes widened in realization. "That SA-X must've plundered our technology," he murmured. "We had an advanced light-bending device…it can be used to camouflage the user and can be linked to a related Chozo-made device – such as Samus' armorsuit. The SA-X made us think that it was Samus and Samus was it…"

"We have to get out of here," Wesley said, his face pale.

"I'll lead us to the ship," Odius said. "The Chozo can carry Samus. Wesley, you keep guard."

-=-=-

Their walk to Odius' ship was uneventful. When they got to the (relatively cramped) spacecraft, they set Samus down on the sole bed. She hadn't moved at all.

"Is she going to…" Wesley began, but he couldn't finish the sentence.

"I don't know," replied Ashen Feather, removing the helmet. Her face was chalk-white, except for the rivulets of crimson blood streaking down her face from the cuts. The Chozo stroked her yellow hair sadly. "I don't know."

Odius seemed the most depressed of all of them. He had been the one to cause this, after all…

As they lifted off and the world of Zebes shrank below them, things could not seem any bleaker.


"Her pulse is getting slower," Ashen Feather said with concern.

He hadn't left Samus' side since they had taken off. Wesley was curled up in the back, trying to catch some sleep. Odius was piloting the ship, his yellow eyes not betraying the guilt he felt at having caused this disaster. White Voice sat in a corner, contemplating something or other. They had dropped off Odius' troops at an outpost earlier; a squad of Space Pirates would be difficult to maintain alongside everyone else.

Odius' eyes flickered from the navigation screen to Samus and back. "We're almost to the hospital," he said. "Drulus should be able to take care of her."

"Are you sure?" Ashen Feather asked. White Voice glanced up keenly. "Because this Drulus fellow, competent as I'm sure he may be, doesn't have access to all the assets that the Federation does."

Odius sighed. "We've already gone over this," he said. "If we take her to a Federation hospital, all of us will be arrested. Besides, I'm sure that Drulus' aid will be enough."

Ashen Feather shook his head. "No. It won't be."

Odius quirked an eyebrow. "It's just a Power Bomb injury. Drulus has treated injuries on par with that in the past."

Ashen Feather shook his head again. "It's more than that." He gently pulled open Samus' mouth and pointed to her teeth. They had become sharp and elongated, almost like a vampire's. "The Metroid DNA is running rampant through Samus' body. Before, it would seem, her willpower was enough to keep it at bay. Now, though, there's nothing to stop it."

Odius stared incredulously at Ashen Feather. "And you expect that the Federation doctors will be able to stop it?"

"At this stage? No. I do not expect anyone to be able to stop it. But if the Metroid DNA runs unchecked, Samus WILL die. It is poison to all living creatures. We Chozo specifically made it so. But there is a chance, however slim, that Samus can survive. We must do everything in our power to ensure that she does. We can always escape from prison; we cannot get another Samus."

"One of us could be at the ready to help the rest escape once the time comes," Wesley suggested. He had woken up in the middle of the conversation, and was now sitting upright.

Odius sighed. "I still think we shouldn't risk it," he said, "but since I'm outvoted…a Federation hospital it is."

-=-=-

Rodriguez's six bodyguards assumed their positions as the ship pulled into the docking bay. Their arrival was top-secret; all precautions had been taken to ensure that nobody that wasn't involved with this business knew of it.

The door to the ship opened up, and two Space Pirates walked out, assuming positions on either side of the door. They were followed by three slow-moving figures, robed and hooded to conceal their decrepit forms. But Rodriguez was well aware of their identities.

At last, the three came before Rodriguez. "Federation President," one of them said in a trembling voice. "We have arrived as per your instructions."

"Search the ship," Rodriguez said to one of his bodyguards. "I want to be certain that there are no hidden troops or weapons."

The bodyguard nodded and moved forward, but one of the three robed figures gripped his arm with surprising strength as he passed by. "What is keeping you from taking control of our ship and taking us hostage?" he demanded. "Can't you just scan the ship to ensure that we have upheld our agreement?"

"Fine," Rodriguez snapped. "Go to the scanning room and search for energy and life signs within the ship."

The robed figure released his hold on the bodyguard, who quickly went to comply with the president's orders.

"Now, what is it that you came here for?"

The three removed their hoods, revealing their wrinkled pirate faces. "You are aware, of course, of the hierarchy of the Space Pirate society. We, alongside Ridley and Mother Brain, are at the top."

Rodriguez nodded. "Of course. The High Command."

"Yes. We recently regained control of Mother Brain, restoring the entire council of High Command once again. But then, to our shock, something unexpected occurred…"

Another of the three High Command members continued. "X Parasites were released on the newly restored Zebes, thanks to the failures of Ridley. A significant portion of our troops stationed there were infected before we managed to convey orders to the remaining troops. Then, Mother Brain herself was infected by the X."

The third one concluded the story. "They sent us an ultimatum: if we did not assist in their spread, then the X would wipe us out. We deliberated the offer for some time; we shared a common enemy, and an alliance with them would be profitable. But we decided against it; the X are too unpredictable to be a reliable ally.

"That's all well and good," Rodriguez said, "but what does this have to do with the Federation?"

A crooked smile crossed their faces. "In lieu of an alliance with the X, we are here to propose a temporary alliance with the Galactic Federation."

Rodriguez did not return the smile. "I don't trust you for the same reasons that you didn't trust the X."

"We essentially put ourselves at your mercy to deliver this message; is that not enough a sign of goodwill?"

"No," Rodriguez responded curtly.

"Very well, then. What if we were to disclose to you all of our scientific breakthroughs…including those in DNA infusion?"

That piqued Rodriguez's interest, but he was still suspicious.

"How are you aware of those experiments?" he demanded.

"I do not know what you're talking about."

"Don't try to play innocent. You specifically mentioned DNA infusion. You know about the experiments we are conducting."

The pirate sighed. "Yes, it is true. We have spies stationed in all sections of the Galactic Federation. You have our guarantee that they will be withdrawn once you accept our offer."

"And how will I know that?" Rodriguez asked. "How will I be certain that ALL of the spies have been removed?"

"Your paranoia is unfounded," the pirate said coolly. "If nothing else, the three true Space Pirates of High Command are honorable. We are willing to assist you in bringing down our common enemy, Samus Aran; we are willing to give you the research we have attempted to use to destroy you. Yet you are not willing to accept our alliance because you are unsure whether or not we speak the truth? Regardless of whether or not ALL the spies are removed, even the removal of SOME would be a huge loss to our intelligence. Think without bias, Federation President; High Command has your best interests at heart."

Rodriguez sighed, placing his thumb, index finger, and middle finger on his forehead as if he had a headache. "And what will I be obligated to do? How will you benefit from this alliance?"

"Our only request is that you assist us in bringing the X Parasite threat under control."

"Fine, then. I'll have a treaty drafted up as soon as possible."

The three pirates of High Command nodded in satisfaction. "Thank you. We will remain within our ship until you have completed the treaty."

-=-=-

"Lord Ridley…a message from the rest of High Command has just arrived…"

The draconic pirate leader swiveled his head around to glare at the poor messenger. "Well? What did they say?"

"They've…just finalized an alliance with the Galactic Federation…they've given us orders to withdraw from Zebes and to await further instruction."

Ridley was silent for a few moments as he digested this information. Then, a dark look came over him.

"No. The Space Pirate Empire shall never lower themselves to working with Federation scum. Those senile old men think that they can just order me around? WELL THEY'RE DAMN WRONG!" he roared.

"Sir, what are you…"

"I'll tell you what I'm planning," Ridley hissed, grabbing the messenger in his claw and bringing him to eye level. "I'm planning a Space Pirate Revolution. The senior members of High Command are no longer fit to rule. They must be killed if the Space Pirate Empire is to survive."


Extra #6: High Command

As we have already mentioned, the Space Pirate ruling body is known as High Command. It is composed of five members: Auros, Ferrix, Duma, Ridley, and Mother Brain. The former three are the senior members of High Command. They were the original founders of the Space Pirate Empire, and originally made all the decisions; however, they were forced to acknowledge Ridley's military prowess and gave him a seat in High Command. Mother Brain's intelligence earned it a seat in High Command, as well.

While all the members of High Command are supposed to be on equal footing, it is actually the senior members who hold the most sway. This is because they agree on most issues; thus, they can outvote Ridley and Mother Brain. While they might take advice from the other two at times, it is ultimately Auros, Ferrix, and Duma who make the decisions. While Mother Brain does not seem to particularly care, Ridley despises this situation.


Extra #7: The Space Pirate Civil War

A rift has been growing amongst the Space Pirate forces, one that threatens to tear the Empire apart. Dissatisfaction with the current government runs rampant, and it was only a matter of time before a war would break out - especially among such a bellicose species.

The release of the X Parasites on Zebes triggered the war, giving the malcontents an opportunity to break off from the main pirate force and begin building their forces. As time went on, more factions appeared, until the current four-way war that we have now became evident.

These are the warring factions in the Space Pirate Civil War:

-Those who remain loyal to High Command - or, more accurately, its senior members. They have formed a temporary alliance with the Galactic Federation to end the insurrections. They believe that Ridley remains loyal to them, but, as they will soon discover, that isn't the case at all.

-The X-Pirates, Space Pirates infected by the X Parasites. They are led by a sort of High Command of their own - the X-infected Mother Brain, and the numerous SA-X wandering Zebes. Their sole goal is to infect the universe.

-Ridley's troops. These are the Space Pirates who believe that the senior members of High Command have lost sight of what the Space Pirate Empire truly is, and believe that Ridley would make a much more capable leader. These are, for the most part, the most vicious troops the Space Pirate Empire has to offer.

-The rebels, Space Pirates who are tired of the endless war against galactic society and who just want to live in peace. This is by far the smallest faction, but there are pirates who share this viewpoint among the main army, as well, but are afraid to turn traitor. It is led by Odius, a former comrade of the deceased General Arvo...