"Samus Aran, previously thought to be dead, was revealed to have survived the attempt on her life earlier today," the reporter read from the paper on its desk. "She was arrested and was en route to her trial when her Space Pirate allies attacked, intending to rescue her. They were successful. Aran's current whereabouts are unknown, but rest assured that the Federation is doing everything in their power to locate her and bring her to justice."

-=-=-

The door behind her opened.

Samus spun around, aiming her arm cannon at the Space Pirate who had just entered the room. It froze in its tracks, yet in its eyes there was some kind of fervent awe.

"…You," said Samus, wondering if she was crazy for trying this. "Can you understand me?" She was well aware that Space Pirates were unable of replicating human speech, but she wasn't sure if they bothered to learn it.

The pirate nodded. "Good," Samus said. "Are there any translator devices that I could use to understand you?" It shook his head. "Figures…" Samus sighed.

"Well, you can understand me, at least. You're going to do everything I say, you got that? I've killed plenty of your kind in the past, and if you betray me, well…one more won't make a difference."

The pirate nodded eagerly. It seemed more excited than before.

"Good. First of all, give me complete access to your network. I want to know everything about your kind's plans."

The pirate scurried over to the computer, its fingers flying over the keyboard. Within moments, a huge list came up.

"Operation Metroid…Project Helix…Phazon Experiments…Operation Super Metroid…" Samus read down the list. It stopped at Operation Super Metroid.

"Where are your current experiments?" Samus demanded. The pirate shrugged apologetically.

"…I don't trust you," Samus growled, pressing her arm cannon to the pirate's head. A small yelp came from it.

Samus instantly retracted her cannon. She hadn't done it with any force…why would it have hurt the Space Pirate? She inspected the inside, but didn't find anything.

So many strange things had been happening…the fangs on her morph ball. Her increased aggressiveness. And now this…

A terrifying thought came to her. What if the Metroid DNA was changing her more than she had initially suspected?

"Urmfshga," a voice said from a loudspeaker. The pirate glanced back at her, then walked out. He beckoned for her to follow.

Samus, now in morph ball form once again, managed to avoid being noticed due to her ally's diversionary tactics. Eventually, they reached a large room with a table in the center. The pirate gestured for her to get under the table.

Samus chose an angle where she could see what was going on. A pirate was carrying a large tray over to the table. After the lid was taken off, Samus could see it was a burnt Space Pirate.

Knives instantly cut the cooked pirate into bite-sized pieces, and the rest of them tore into the meal ravenously. Bits and pieces of the meat flew everywhere. For the hundredth time that day, Samus felt that she was going to be sick.

An eyeball fell under the table alongside Samus to keep her company.

-=-=-

"Threatened to kill me don't send me to prison please I didn't want to help her she made me do it I wanted to live please please it's not my fault!"

Even as Federation troopers escorted him to the president's office, Tarus Wesley kept on babbling on about why they shouldn't arrest him. They were quite happy to get rid of him once they reached it.

Rodriguez was inspecting a paper when Wesley was unceremoniously thrown into his office. "Have a seat, Mr. Wesley," he said without looking up. "We have much to discuss."

Wesley meekly crawled into the chair and stared at the Federation president.

"Now," he said. "Tell me everything that's happened."

Wesley opened his mouth. "Well, you see, Samus got out of her ship but I didn't notice and she went to my ship and entered it and threatened to -"

"Slowly," said Rodriguez dryly.

"…Right. Slowly. I can do that. Samus threatened to kill me if I didn't report her as dead…I didn't have a choice. She told me to get her onto the Valhalla. I didn't have a warrant, so her shipboard computer – its name is Adam, I don't know why its name is Adam – impersonated you and let me on. Samus showed me what you were doing there…"

Rodriguez nodded slowly. "Yes…those things," he murmured.

He stood up. "Well, you already know of them, so you might as well know their purpose. Project Werehuman is a Federation DNA splicing program meant to bring down the Space Pirates once and for all. We are essentially creating the ultimate supersoldiers – we intend to put every deadly asset into the human body. The Space Pirates have proven time and time again that they are more powerful than us, so we naturally are using them in the process."

Rodriguez grinned. "We also recently obtained a certain DNA sample that I'm certain will drive us to victory…tell me, have you ever heard of the Chozo?"

-=-=-

They had landed.

Samus wasn't entirely sure what planet they had landed on – based off a brief glimpse out a window, it was a jungle environment – but they had certainly landed. Her ally, knowing not to risk capture, had gone with them, and now Samus was waiting for the ship to empty out.

Normally, she could access the Federation databanks via her suit to find out where she was, but that was dangerous – they might be able to pinpoint her location if she connected to them. She'd have to figure it out on her own.

Before leaving the ship, however, she took the arm of her armor off, as she had done every twenty minutes for the past few hours. She was searching for any sign of the Metroid DNA further overtaking her.

As she gazed at her hand, her blood ran cold.

All of the fingers of her left hand were translucent. The fingernails had formed claws similar to Metroid fangs.

Samus shuddered, then headed outside. She couldn't let this interfere with her mission.

She would continue her mission even if she became a full Metroid.

The dense foliage helped to conceal Samus from the eyes of the pirates guarding the building. It was a grey stain on the green paradise, pumping noxious fumes into the air as the Space Pirates conducted their sinister business within.

Somewhere in there, Samus's ally was preparing to let her inside.

She didn't have to wait long; she spotted the renegade pirate as he exited the building, knocking both of the guard pirates out with a solid blow to the head. The pirate gestured for her to hurry. Samus made no arguments.

As foreboding as the building was on the outside, it was even more frightening on the inside. Flickering lights were all that illuminated the dilapidated facility, occasionally allowing glimpses of the mutilated wildlife that had accidentally wandered inside, only to be mauled by pirates. There were no windows.

The snarls of Space Pirates approached the two of them. Samus froze, as did her ally. There was no place to hide…!

She had no choice but to fight.

Four pirates rounded the corner, only for one of them to be met by an ice beam to the face.

The other three sounded the alarm.

Samus cursed her luck and began firing at the remaining pirates. Her ally went in for close combat, distracting one of the pirates from its allies as both of them were frozen and promptly shattered. Her ally stuck its wrist-scythe into the enemy's torso, then pulled it out.

More pirates rounded the corner.

Samus's ally once again began fighting, while Samus picked off the rest from afar. She had killed hundreds of Space Pirates before, and she was getting into the groove of it again.

She no longer had to concentrate.

Three left…two left…one left.

She fired off the last shot…just as she realized that the remaining pirate was her ally.

The pirate tried to dodge, but it was no use; he was dead as soon as the beam hit him.

Samus felt numb.

-=-=-

"The Chozo?" repeated Wesley slowly. "But didn't they disappear years ago without a trace?"

Rodriguez nodded. "Correct. But one trace of them remains."

"I don't get it."

Rodriguez sighed. "Haven't you ever wondered why Samus Aran is so powerful? Haven't you ever wondered where her suit came from?"

Wesley slowly began to connect the dots. "So…her Power Suit is Chozo-made?"

Rodriguez nodded, smiling. "Not only that, but Aran also has Chozo DNA within her. During an operation on her, we managed to get a sample of that DNA. We can now use it in the project." He seemed quite pleased with himself.

Wesley hesitated.

"…On a completely different note," he said slowly. "You reported that Samus Aran was an ally of the Space Pirates. That's not right. That can't be right."

Rodriguez's smile faded.

"…There's no way to tell for certain," he admitted. "Whether or not she's allied with the Space Pirates, though, she's no longer on our side. She is a threat to the Galactic Federation, so she must be killed. And if telling the people lies is what it takes to get them to hate her, well…" He shrugged.

"I understand," said Wesley.

Rodriguez's smile returned. "I'm glad. Now, I have a question for you…would you like to get revenge on Aran for threatening your life?"

Wesley seemed startled. "Uh…sure?"

"Excellent," Rodriguez said. "Glory will be yours if you capture her. Now, allow me to introduce you to someone who can help you find her."

Turning back to his desk, he typed out something on his computer. A metallic voice that, for some reason, sounded familiar to Wesley responded. "Galactic Federation AI 3240 responding. Awaiting orders."

"This," said Rodriguez, "was Aran's shipboard computer. We retooled it to be completely loyal to us. It's stilled connected to her Power Suit, though, so we can track her from anywhere in the galaxy. Let's see where she is now…"

Rodriguez turned back to the computer. "AI 3240, requesting coordinates of Samus Aran."

"Scanning…done. Coordinates of Samus Aran are: 45, -3691, 994, 23. 34 LAT, 92 LON."

"See?" Rodriguez said. "Now, we just type them in and find out where she is, then we can…"

A look of confusion crossed his face as the results came up.

-=-=-

Samus's heavy footsteps pounded through the building. The pirates already knew she was there, so there was no point in stealth.

She regretted killing her ally, but she hadn't exactly known him very well. As a result, she didn't feel much sadness for him. Perhaps she'd feel more sorrowful when her life wasn't in jeopardy.

Samus turned another corner…and reached a dead end. There was only a single door at the very end of the hall.

Seeing no other options, Samus approached the door. It was locked, but a keypad was right next to it. In the past, this would have been no trouble; her suit had once contained the single most sophisticated hacking system in the galaxy. However, that had been one of the components of her suit lost when an X Parasite attacked her.

Hearing more pirates approaching, Samus did the only thing she could think of – she smashed the keypad with her fist.

Much to her pleasure, the door opened.

Samus walked inside, looking around the room. Equipment was strewn all over the place, along with a strange machine along the sides. Several wires ran from the machine to a stasis chamber at the back of the room.

Samus, her curiosity piqued, walked to the stasis chamber and peered inside.

It was an exact copy herself.

Samus leapt back, then composed herself again. No, it wasn't an exact copy. This Samus wore her original Varia Suit. It was probably just an empty shell; possibly an experiment by the Space Pirates to replicate her Power Suit.

Then it moved.

The Samus within the tank clenched and unclenched its fist.

With a feeling of dread, the real Samus recalled Adam's words aboard the B.S.L.:

"There are now no fewer than 10 SA-X aboard the station…"

Everything was coming together.

The Space Pirates weren't only aboard the station because of the Federation's heinous experiments; they had actually infiltrated it. Samus wasn't sure why, though. Most had been infected by the X Parasites, but some of them must have escaped infection. They captured one of the ten SA-X – or, perhaps, Samus thought, made an alliance with it – and escaped before she destroyed B.S.L. and SR388.

Either way, one thing was for certain: her work had been for nothing. The X Parasites had survived, and now the most powerful one of all was right before her.

The only thing that didn't make sense was what Ridley had been doing in cold storage on the B.S.L.

As if on cue, a certain fearsome space dragon, barged into the room along with dozens of Space Pirate reinforcements.

Samus instantly whipped around, aiming her arm cannon at Ridley. One of the Space Pirate reinforcements fired at her prematurely, but it was promptly dealt with by an Ice Beam to the head.

"Ridley," Samus growled, feeling her rage boiling up inside of her. She had killed him time after time, but he was always revived by the Space Pirates.

"Aran."

Samus was momentarily surprised; she had known that Ridley was capable of speech, but he had never spoken a word to her since the day he had killed her mother. Then again, she noted, they were too busy trying to kill each other to exchange conversation.

"Are you aware that the Galactic Federation is attempting to pass you off as one of us?" Ridley asked. "You? The self-proclaimed 'defender of the galaxy'?" The Space Pirate leader laughed, finding the very idea of it to be too humorous for words.

Samus said nothing, feeling her anger surge through her. Killing him now would accomplish nothing, though…the Space Pirates would just revive him like always. Better to try to glean extra information from him.

Ridley's laughter stopped. "You and I both know that would never happen, of course," he said, his voice dying down to a whisper, "but they don't."

What in the world was he talking about?

"What were you doing in cold storage on the B.S.L.?" Samus demanded, changing the subject.

Ridley's eyes went dark with anger. "That wasn't me," he snarled. "It's none of your business, anyway."

As if to make his point, Ridley shot a fireball at her. The troops, taking this as a signal to open fire, shot at Samus as well. Much to her confusion, however, Ridley swept them all against the wall with his long tail. "Don't kill her!" he roared.

"Why…?"

The space dragon turned back to her, a devilish grin on his face. "Our sensors detected Metroid DNA in this building. Now, we no longer have any Metroids, so this had to have come from the outside. We tracked the Metroid DNA to this very room, and, well…" He gestured at Samus. "Here you are."

Samus frowned. "I don't understand."

Ridley's eyes gleamed. "You remember what happens when Metroids are exposed to beta rays, don't you?"

Samus wracked her memory for that specific piece of information. Her eyes widened as she remembered it.

"…They asexually reproduce…" she murmured.

"Precisely. We don't know what'll happen when we expose you to beta rays – after all, you are part-human and part-Chozo – but it's not as if we have anything to lose."

Samus suddenly had a feeling of dread. She had to escape…now. But there was nowhere to go. The only exit was blocked by Ridley and the Space Pirates. Her only option was to stall them even more.

"The SA-X," she said. "Where'd you get it?"

"SA-X? Is that what you call it?" Ridley snorted. "We found it drifting within a jettisoned portion of the B.S.L. It had almost been eaten alive…the Metroids that had almost killed it were dead, though. We took it and brought it back to our base here. We're doing extensive study on it before releasing it."

"Where is 'here'?" Samus asked.

Ridley grinned. "You should know that better than anybody, Samus. We're back on Zebes."

-=-=-

"Zebes?" Wesley repeated. "Didn't it explode?"

Rodriguez nodded, just as perplexed as him. "It did…"

"Maybe she's just in the place Zebes once was?" suggested Wesley.

Rodriguez shook his head. "No…if that was the case, the computer wouldn't have given us her latitude and longitude."

"Well, then…I guess I better get going to see what's going on, huh?"

Rodriguez grinned. "Bring Samus' armorsuit for me, will you? I've always wanted to study it up close…"

-=-=-

"How did you bring Zebes back?" Samus demanded. "It exploded. I made it explode. Nothing even remained of it!"

"No more questions," Ridley replied. "You've stalled for long enough."

The Space Pirates moved forward to capture her. Samus stepped back, accidentally knocking into the tank containing the SA-X.

And then she did the only thing she could think of.

She unloaded a missile into the tank, shattering the glass and freeing the SA-X.

"No!" Ridley screeched.

And then she fled.

Blowing through every pirate in her path, she raced to the room's exit, not bothering to look back and find out what was happening. With luck, the SA-X would simply kill all the pirates and make things much simpler.

If she wasn't so lucky, the SA-X would become allies with the Space Pirates, and she shuddered to think of the consequences of that.

Loud explosions and shouts followed her path as she raced through the halls. She had to get out of there quickly. The exit was right there...!

And then the emergency shutters closed.

Samus kept running, reaching down into her latent abilities. And then, suddenly, she was faster than the wind, literally ripping through the shutter as if it was paper, out into the open air. "Thank you, Speed Booster," she chuckled, but her euphoria at victory only lasted a moment. The ceiling of the building broke off, and there was Ridley again, screeching as if all hell had broken loose. In a way, it had.

It took only a moment for the space dragon to spot Samus, and then he dived for her. Samus quickly leapt to the side, firing off a shot as she did so. It hit Ridley's left eye, freezing the skin around it. Ridley screeched again and shot off several rounds of fireballs. Samus rolled into morph ball mode to allow for better maneuverability, but several fireballs scorched her nevertheless. She returned to normal form to look at her energy display.

Three and a half full energy tanks.

She turned to face Ridley again, this time firing off a missile. The airborne beast dodged it easily, swooping down to attack her again. Samus once again dodged, but this time, Ridley's outstretched claw raked her, cutting through her armorsuit to the vulnerable flesh beneath. Samus cried out, falling to one knee. Ridley took this opportunity to pick her up by the head.

Ridley raised her to his face, his grip around her tightening. There was a sort of wild delirium in his eyes. "You have no idea," he hissed, "no idea how long I've been waiting to do this."

Flames began to form in his mouth. Samus only had one energy tank left now, and it was dropping by the moment due to Ridley's grip…there was no way she would survive this next attack.

She struggled, attempting to get free. She grabbed ahold of Ridley's arm, trying to rip it loose.

Much to her surprise, as she gripped it, she felt herself getting stronger.

Ridley's attack faltered, and his grip weakened. "What…?"

Samus, realizing what was going on, only tightened her own grip. At the same time, she took the armor off her hand, revealing the Metroid-like hand within. The claws dug into Ridley's flesh, and she felt herself draining his life-force.

Luck was on Ridley's side that day, though, as a band of pirates had exited the building. Seeing their leader in trouble, they fired upon Samus, causing her to lose her grip. The two fell to the ground, and Samus promptly ran into the foliage, leaving the pirates behind.