AUTHOR'S NOTE: I apologize for the formatting of recent chapters, but I seem to be having a bug with my mobile uploads.

A New Threat

Everyone stood frozen as Metroid Prime emerged from the portal, still wearing Samus' Phazon Suit. Jake could feel Samus' surprise through their mental link, knowing that she had believed Prime to be dead. Jake didn't dare to take his eyes off of Prime, having read through Samus' reports from previous encounters with it. It was just as well, for Prime launched a Phazon charged Super Missile at the pair with the same suddenness as her arrival in the Great Temple's main chamber. Jake caught the projectile, pushing Samus back as he felt the Phazon's energy become unstable.

Samus watched in horror from the floor as Jake was consumed by an immense blast that sent her skidding across the chamber. U-Mos picked her up as she came to a stop near his feet. They watched on, blood freezing in their veins as they heard Jake roar from within the cloud of debris. Samus worried that such a powerful Phazon blast would make him revert to his feral state, like the damage he had sustained inside the Crater on Tallon IV, or the charged missile he had used to destroy the Phazon infused Ridley.

Jake's armor was giving off a crimson glow when the dust settled, much like it had when he fought against Ridley. The ground beneath his feet cracked as he launched himself at Metroid Prime, claws extended and charged with Plasma energy. The impact sent them flying into the far wall, Jake unrelenting in his enraged state as he continued to batter at Prime, shattering the wall behind it. He refused to allow Prime to escape, his hand shooting out and gripping its helmet to prevent it from falling to the ground below as the wall crumbled. He tossed Prime back into the chamber, not realizing that it had come to a stop near the portal. As he closed to finish Prime off, it tripped him by kicking his legs out from under him, sending him stumbling into the portal before jumping in after him.

"Jake!" Samus screamed as she dashed towards the portal, but it closed before she could reach it, leaving her staring at the empty space in horror.

"I believe he will be able to handle himself, and that he will likely return," U-Mos suddenly said from beside her, causing her to jump.

"I don't doubt his combat abilities, I'm worried what the atmosphere of Dark Aether might do to him," Samus answered as she continued to stare at the space the portal had just occupied.

--

Jake rose from the ground, shaking his head to clear it. He felt dizzy as he looked around and saw the Great Temple, the sudden changes in the architecture and colors throwing his dazed mind for a loop. It was only when his eyes fell on Metroid Prime, kneeling near a large hole in the wall to consume Phazon from the ground, that he remembered what had happened. He let loose a terrible growl as he began entering his Lupus form, causing Prime to turn around. Jake's growl died in his throat as he beheld Prime's face.

The metroid had taken on Samus' physical appearance, not only her armored form. Jake stumbled forward half a step as he saw Samus' face staring at him, the only difference being her ghostly blue color and yellow eyes.

Jake couldn't wrap his mind around what his eyes were seeing, his shattered focus causing him to revert to his human form.

"Why do you look like Samus?" He asked aloud, unable to contain the thought looping through his mind.

"Her DNA must have been bonded to the suit that I took from her, I have yet to find a different explanation," Prime replied, even its voice was nearly identical to Samus'.

Jake was too stunned to speak, he just stood staring at this strange image of Samus. After all of the reports he had read, nothing could have prepared him for this.

"Why didn't you kill me while I was down? Why aren't you trying to kill me now?" He finally blurted.

"I need your help," Prime replied, surprising him further.

"What could you possibly need help with?" He asked in amazement. He knew Metroid Prime was a formidable creature.

"The Space Pirates found a way to sneak back into Dark Aether. They've been experimenting with infusing both Phazon and the parasitic Ing into various creatures, including themselves, to use as weapons. On top of that, they seem intent on capturing or killing me," Prime explained, it's anger contorting Samus' face into expressions Jake had never seen.

"Why should I believe you won't just turn around and kill us afterward?" Jake asked, still unable to believe he was having this conversation.

"It's a win-win. I no longer have to worry about being hunted down by them, and you two get to save Aether. I just want to be left alone," Prime said, its expression sad as it finished.

"Do we have a deal?" It asked, suddenly becoming serious and angry again.

"We have a deal," Jake replied after giving it some thought.

"But know this, if you try anything to harm Samus, I will kill you," he added in a growl, the crimson glow of his eyes visible through his visor.

"You have my word," Prime said, holding its hands up.

"For whatever that's worth," it added in a mutter that Jake only heard because of his enhanced hearing.

"So how do we get back?" Jake asked, changing the subject.

"Beats me," Prime said with a shrug.

"I just jumped into the portal when I saw it," it added in explanation.

Jake looked around and spotted an odd machine in one corner of the room. He scanned it with his visor and nearly jumped for joy when he discovered it was a portal machine. He ran over to the machine and searched for a way to activate it. Another scan revealed that it had no power supply, and required a Light Beam shot to start.

"Don't know how we'll get one of those," Prime said when Jake shared his findings, not seeing his smile behind his visor.

Jaked stepped in front of the portal platform, raising his right hand and charging it with Light energy. A small ball of light appeared in his hands, brighter than any charged Light Beam shot. He flicked the ball into the faint ripple he could see by its light, blinking to clear his eyes as the portal appeared with a blinding flash.

"Neat trick," Prime said as she walked up to stand beside Jake, who knew that its tone would have been flirtatious coming from Samus.

He stepped through the portal with his hands raised, Prime following behind him in similar fashion.They emerged almost instantaneously back into the Great Temple's main chamber, Samus and the Luminoth standing around the portal with weapons raised and ready.

"Hold your fire!" Jake called as he saw the scene before him.

"Jake!" Samus shouted, ignoring Prime and running to him.

She wrapped her arms around him and pressed her head against his chest, glad beyond words that he was back and safe. She spotted Prime over his shoulder, jumping back and positioning herself to battle her old foe.

"Wait," Jake said, putting his hand on her shoulder.

"For what?" Samus asked in disbelief, never taking her eyes off Prime.

"It wants to team up to take down the Space Pirates, and then it wants to be left alone" Jake told her.

"You can call me by 'she' instead of 'it'," Prime said in annoyance, causing Samus to stagger back in disbelief.

"Show her," Jake said to Prime, indicating she should remove her helmet.

Samus nearly fell when she beheld Prime's face, would have, if Jake hadn't caught her. He could feel her shaking in her armor, could feel her shock and fear through their link.

"How?" Samus finally whispered. Prime gave a sigh before explaining, going on to tell Samus all that she had told Jake.

"Give me one good reason why I should trust you instead of killing you where you stand?" Samus asked her dark counterpart.

"Because of him," Prime said, pointing at Jake.

"He could destroy entire planets by himself, even if he doesn't realize it yet. I'm not stupid enough to go against him," she explained, surprising all present. Not a soul alive would have believed that Metroid Prime feared any other creature.

"He already made it quite clear that he would destroy me if I do anything to harm you," Prime added.

That, at least, made Samus a little more comfortable. After what Jake did on Tallon IV, every time she was in any danger, Samus knew beyond a doubt that he would destroy a planet if it meant protecting her. Jake suddenly called out to her mentally, using their link to show her his own memory of talking with Prime, just as he had done with the jewels of their Power Suits on Tallon IV. After seeing Jake's memory, Samus lowered her weapon.

"I guess we're teaming up for now, then. You'll have to meet up with us somewhere along the way. We can't risk the Federation getting involved if we're going to work together," Samus said, her tone anything but friendly.

"Fine by me," Prime said before putting her helmet back on and stepping back through the portal to Dark Aether.

Samus fired a charged shot from the Dark Beam into the portal's center as Prime's back disappeared, forcing it to close behind her. She turned to look at Jake as he took on his wolf form and nudged her towards the door. The door had just closed behind them when Federation officers stormed them with weapons drawn. Jake growled menacingly as they surrounded him and Samus, their weapons aimed at the pair.

"Samus Aran and Jake Lupus, by order of the Galactic Federation High Command, you are both under arrest. Surrender yourselves peacefully or we will be forced to take you down," one of the Federation officers said in a commanding tone.