Location: G.F.S. Atlantis, Solar System

Meanwhile, the crew on the Atlantis learned of a shocking development.

"What? An X Parasite?" Admiral Picard asked in astonishment.

"Yes, sir." One of the Marines answered. "A team of researchers came upon it while investigating the remains of SR388."

"I thought that they were all destroyed when the BSL Station collided with SR-388, but apparently, one survived." Picard said.

He looked like he was thinking hard about something.

"Sir? May I ask what you're thinking about?" The Marine asked.

"I'm thinking that we could use this X Parasite. Have the researchers collected it?" Picard asked.

"Yes, sir, they have." The Marine answered.

"Good. Contact them and tell them to create another Samus clone, one based off the SA-Xs." The Admiral directed.

"Um… Another clone, sir?" The Marine asked doubtfully.

"Don't worry. We'll make sure this one doesn't have a mind of its own." Admiral Picard reassured.

"Understood, sir." The Marine said before walking away.

Admiral Picard looked out into space.

"It won't be long now. Soon, those traitors will get what's coming to them."

Location: Chozo Ruins, Tallon IV

While this was going on, Sarah and Sammy approached where Samus was sitting. They stopped at the end of the half-pipe opposite to where Samus sat, Sarah putting a protective arm in front of Sammy. Samus stood up and pointed her arm cannon at them. They tensed up, their right hands next to their blasters. Samus looked at them. One of them looked just like her, except the clone had darker blue eyes and her long black hair was down. As Adam had described before, the other one had the appearance of a child, one not unlike herself at that age. However, the younger clone had green hair and red eyes. Samus found that strange. Speaking of the girl's eyes, another thing Samus found strange was that they showed no malice or intent to fight her. Her curiosity got the better of her and Samus looked back to the older clone.

"Adam told me you might work for the Federation. Is this true?" She asked.

Samus' question took Sarah by surprise.

"They created us, yes. But, no, we don't work for them. If anything, they're after us." Sarah said.

Samus was very surprised by that answer.

"Why?" She asked.

"We reduced the scientists that created us to brittle husks and ran off." Sarah said.

Samus was confused.

"What was your purpose?" She asked.

"The idea was for us to take you down and bring you back to HQ with us. We weren't too thrilled about doing that, so we betrayed them and decided to help you instead." Sarah explained.

This just made Samus more confused.

"Wait. I'm really confused now. Why on Earth would you betray your own creators? Why help me?" Samus asked.

Sarah's answer was simple.

"Because we were created from two Metroids you know very well." She said. "You can probably guess which based on our appearances."

Samus thought a little, then gasped. After regaining her composure, she immediately pointed her arm cannon at Sarah's head.

"Is there no way to kill you?" Samus asked venomously.

"Point that thing somewhere else. I already told you that we mean you no harm. Besides, shouldn't you be asking Ridley that question?" Sarah said.

"Why should I trust you?" Samus asked.

"I'm not driven by an appetite for Phazon anymore. My mind is clear now. I know what I did was wrong. I know apologizing's not going to bring the bounty hunters or anyone else back, but neither is killing me where I stand." Sarah said.

"It may not bring them back, but I will still avenge them!" Samus said.

"Mama! Stop!" Sammy yelled as she got in front of Sarah. "If she really was Dark Samus, I'd be dead right now! And so would you!"

"This doesn't concern you, little girl! Now, move it!" Samus yelled.

"She's right, Sammy! This is between her and me! I don't want you to get hurt!" Sarah said.

"No! You helped me to walk! You helped me to talk! You even promised me a reunion with the woman I imprinted on! The woman that spared me the fate of my brethren on SR388! The woman who tried and failed to protect me from the Space Pirates! The woman I almost killed inside Tourian and later sacrificed my life for in order to defeat Mother Brain! Even if she was never my real mother to begin with, I still wanted to see her again! You gave me that chance! After all you've done for me, I'm not going to stand here and let you be killed!" Sammy protested.

"Sammy." Sarah muttered.

This threw Samus for a loop. Could it really be? She shook her head.

'No.' She thought. 'There's no way. It's just a trick.'

She redirected her arm cannon at Sammy.

"If I have to kill you first, little girl, then so be it!" Samus called.

"Fine! I didn't want to do this, Samus, but you leave me no choice!" Sammy said.

She took her blaster out, but instead of firing it, she tossed it aside. This confused Samus. Then, suddenly, Sammy launched herself at Samus' head, knocking her over. She then dug her fangs into Samus' helmet. Sarah was wide-eyed as she realized what Sammy was doing. Samus, meanwhile, was shocked as the energy levels in her suit dropping. She then remembered what Sarah had said about Sammy and her being created from Metroid DNA. Samus then took initiative and curled up into Morph Ball form and started dropping bombs. But, oddly enough, Sammy wouldn't let go. The Power Suit's energy levels continued to drop. It wasn't until the suit's energy levels were almost nonexistent did Sammy finally let go. Samus was uncurled and on one knee, like she was when she was severely weakened by Mother Brain's Hyper Beam. Sarah was still in shock. Sammy walked around Samus and knelt down in front of her to look her in the eye. She let out a light laugh, despite her guilt.

"This is familiar, isn't it? I drain you of your energy, leaving you within an inch of your life. Only, in Tourian, it was by accident, while here, it was on purpose." Sammy said to Samus.

"How do I know… that you're… the real Baby? That this… is not… some sort of… trick?" Samus asked breathing heavily.

"Well… I've saved your life, twice I remember right." Sammy said.

"I knew it. You're not the Baby. The Baby only saved my life once." Samus said after catching her breath.

Sammy was confused.

"But, I did save your life twice, didn't I? The first time was attacking Mother Brain, and the second time was through the Metroid vaccine that saved you when that X Parasite infected you." Sammy replied.

"But, the Baby wouldn't know about the vaccine. It died before then." Samus countered.

"Which is why we looked at the Federation's record of your activities before we got here." Sarah spoke as she walked over and knelt down so she could look Samus in the eye.

"What?" Samus asked.

"While we were in hyperspace on the way here, I was curious as to what you did after Phaaze was destroyed. So, I checked the Federation's records of your activities. I didn't expect to get your whole history, from Zebes to the BSL Research Station. You've had a rough life, Samus. Kind of like me." Sarah said.

"Wait. Why the hell would you need to look into the Federation's records? Surely, you would've known all of that already from what the Federation told you." Samus said.

"Please. The Federation didn't tell us anything. They never got the chance to. I already told you that we betrayed the Federation. We escaped before they could tell us anything. It was Aurora Unit 242 that led us to you." Sarah said.

"242?" Samus asked in surprise. "Wait, I thought you said the Federation didn't tell you anything."

"Not the scientists who created us, or the Federation itself for that matter." Sarah clarified.

"I see. But, wait, if you two betrayed the Federation, why would an Aurora Unit help you? They're loyal to the Federation." Samus asked.

"Not to the ringleaders, they aren't. 242 made that clear. And, I doubt an Aurora Unit would lie to us. With 242 and 313 serving as examples, they seem to have wills of their own." Sarah concluded.

"You know what? You have a point there, Dark Samus." Samus admitted.

Sarah grit her teeth at the name.

"We have actual names, you know. I'm Sarah and the little one is Sammy. Aside from another chance at life and the clothes on our backs, those names are the only things the scientists gave us that we're grateful for. Well, their life energy too, but we technically took that ourselves." Sarah said.

Samus made a face.

"What? How would you feel if you bore someone else's name for a long time? Metroid Prime was better, because that moniker didn't make me feel like a copy of someone else." Sarah said.

"Why do you care so much about that?" Samus asked.

"Because I don't want to be 'Dark Samus' anymore. I want to feel like an individual, my own person. Besides, the name doesn't suit me anymore." Sarah explained.

"You still haven't proven to me that you've changed." Samus said.

"That's true." Sarah agreed, looking down.

Sammy looked at her sadly. She turned to Samus.

"I am your Baby, whether you believe it or not, Samus." She said.

Before she could say anymore, she noticed something in the corner of her eye. Whatever it was seemed to be getting brighter. She gasped when she realized what it was.

"Mama! Look out!" Sammy cried as she launched herself at Samus again.

Samus was knocked over again and prepared to go to Morph Ball mode again. Suddenly, an energy blast shot past them. Looking toward where the shot had come from, Sarah saw a Pirate Trooper growling as he had missed the Hunter. She wasted no time and blasted him to the ground. She then ran over and pinned him before he could get up, holding her blaster to his head. Meanwhile, Samus lie in surprise that the child claiming to be the infant Metroid had saved her, instead of draining her energy this time.

"Sorry about that, Samus. Are you all right?" Sammy asked.

"My energy is still low, but I'm fine." Samus answered.

Samus thought for a second.

"Speaking of which, that shot probably would've done me in, so thank you." She said.

Sammy giggled.

"So, I've saved your life again? One of these days, you should save me, or someone else for that matter. But," she trailed off sadly, "everyone you've tried to save ended up dead. Me, Adam, the Chozo, Rundas."

Samus found it harder to deny that this was, in fact, the Baby reincarnated. Sammy seemed to care for her very much and had just saved her from near-death. Not to mention she called Samus "Mama" at least twice. While this could still be a ploy to get her to let her guard down, Samus seemed to see something in the girl that spoke of nothing but benevolence, so she decided that it wasn't a trick. However, that was not important at the moment. What was important was the Pirate Trooper. What was he doing there? How did he find her? Come to think of it, how and when did he arrive on Tallon IV? Why, for that matter? Questions like this buzzed around Samus' head. Sarah started the interrogation, bringing Sammy out of her thoughts and causing her to look over.

"All right, you scum, why are you here?" She asked.

"That's none of your business, you wretch!" He growled in his native tongue.

Sammy was the only one at a loss as to what was said, because Sarah had led the Space Pirates as Dark Samus and Samus had a translator in her helmet, which still functioned even after Sammy had drained her. Sammy, meanwhile, had only learned bits and pieces of the Pirate language while in captivity and thus didn't have a complete understanding of it like Sarah and Samus did.

"I say that it is my business, you bastard!" Sarah countered. "Now, I'm going to ask again! Why are you here?!"

She shoved her blaster into the Pirate's face, frightening him.

"A-a-all right!" He cried at last. "I'll tell you! When we discovered that the Hunter was headed here to Tallon IV, we followed! We wanted revenge for her destroying our glorious leader, Ridley, along with Mother Brain and the rest of our kin on Zebes! Down with the Hunter and glory to the Space Pirates!" He finished with a roar.

Samus was taken aback for a moment because she didn't think there were still Pirates after she defeated Mother Brain the second time. The only Pirates she had encountered recently were the Zebesians created by the Federation as bioweapons. Seeing a real Pirate in the flesh proved that the Space Pirates had not died out as was previously thought.

"Well, you won't lay a hand on Samus! Not while my friend and I are here!" Sarah said.

"Ha! What could two Earthlings like you do against us?" The Pirate scoffed.

Sarah chuckled darkly at this.

"But, that's the thing, you piece of garbage. My compatriot and I are not ordinary humans. We're clones made from Samus' DNA and Metroid DNA. That makes us just as much of a threat to you as Samus." She said.

The pirate shivered.

"Clones of the Hunter? One was bad enough! And combined with Metroid DNA? Even worse!" The pirate squealed.

Sarah's smirk grew larger as she thought of what she was going to say next.

"It gets even worse." She said sadistically. "I used to be Dark Samus."

The pirate trembled in fear at this.

"T-t-the D-Dark Hunter r-r-returns?" He stuttered.

Sarah was grinning like the Cheshire Cat now.

"Yes, she does." She hissed.

Before the Pirate could scream bloody murder, Sarah blasted his head off, splattering blood everywhere. Sammy went pale. She knew Sarah had suggested draining the scientists dry before, but she never thought about Sarah being this sadistic. Samus put a protective arm in front of her and aimed her cannon at Sarah almost immediately. Sarah turned to them. Some of the Pirate's blood had splashed onto her face.

"I knew it. You haven't changed at all. You're still a murderer." Samus said in anger.

Sarah's smile dropped as she realized that Sammy had been watching the whole time. She opened her mouth to apologize, but Samus shot her with her Ice Beam before she could say anything, freezing her solid. This proved that what Picard had said earlier about Sarah and Sammy having the Metroid affinity to the cold was true. Samus then prepped a missile. Sammy gasped, recognizing the age-old strategy of disposing of Metroids, and shoved Samus' Arm Cannon aside, causing the missile to fly towards a wall and hit it. Samus was shocked and still angry.

"Why do you continue to protect her?! You saw what she did to that Pirate!" Samus yelled.

Sammy glared at her.

"I wouldn't have made it off Earth if it wasn't for her!" Sammy yelled back.

"But…" Samus started before being interrupted.

"I did see what she did, Samus! But, don't you think you would've blasted his head off too?! We both know how much you hate Space Pirates!" Sammy countered.

Samus faltered, because she would have done that too. Sammy wasn't finished though.

"Sarah's also the reason I can stand on two legs and speak properly! She could've left me in that lab, helpless as I was! She could've just let the Federation have me and be on her way! She promised me a reunion with you!" She yelled, with tears in her eyes.

She fell to her knees and supported herself with her hands, facing the ground with tears streaming down her face and falling to the ground.

"Maybe coming here was a waste of time." She got out before sobbing.

Sammy wasn't used to having human emotions and could barely control them. Samus didn't know what to do, because she wasn't trained for this kind of situation. But, even then, something inside her made her want to comfort the poor girl. Samus recognized it as the same thing that made her want to spare the infant Metroid and rescue it from the Space Pirates. While on her trek through Zebes, Samus had realized that it was some sort of maternal instinct, like the Metroid really was her child, even though it was never her flesh and blood. Samus was confused at first as to how this instinct had returned. Then, she remembered that the girl in front of her was the Baby reincarnated. Realizing that Sammy was more her child now because of their shared genetics, Samus felt it was right to act as the girl's mother again. However, Samus still wasn't used to these situations and just awkwardly embraced Sammy, letting the girl cry into her armored shoulder. Sammy was surprised by this gesture, but was still crying and simply appreciated it.

Samus looked over at the ice block that contained Sarah. She didn't want to admit it, but she felt a little guilty after Sammy berated her for freezing her companion and not giving her a chance. Now, Samus had her Plasma Beam on hand, but Samus deemed it too risky, because one blast might shatter Sarah's body completely. If that happened, Sammy would be so upset that she would kill Samus without hesitation. As a result, the Galactic Federation would continue making bioweapons and the galaxy would be doomed should the horrid things somehow escape. Needless to say, it wouldn't benefit Samus at all. Besides, the thought of Sammy hating her made Samus feel uncomfortable. Samus figured it was her bond with Sammy that made her feel this way, as she was the girl's adoptive mother.

Soon, Sammy had exhausted her self from crying and fell asleep. Samus held her like she was an infant. It made sense, considering that Sammy appeared to be at least 3 years old. Thinking it was best, Samus decided to return to her gunship. So, she used her Grapple Beam to grab a hold of Sarah's frozen body and dragged her back while holding Sammy in her arms.