This story narrates the events following Metroid Fusion. Welcome to Metroid 5.
This plot seems highly unlikely, but I wanted to explore what could happen if Samus joined up with the Space Pirates. As of right now this story is incomplete.
Chapter 1: Corruption
Samus awoke in an unknown bed with the worst headache of her life. Scratch that, worst body ache of her life. Pain radiated from almost every inch. It hurt to even blink.
A system check revealed that her power suit was deactivated, though not damaged. Surprising, given the magnitude of the blast which occurred at BSL and SR388. In fact, all of the Chozo technology was functioning at 100% capacity, with just two anomalies reported: the suit was no longer permanently bonded to her body, and there was no longer any Metroid DNA in her blood.
"Ah, you have finally woken up." said a voice in Pirate language. A scientist, accompanied by a Commando, approached the bed side, both smiling. Still too tired to speak, Samus remained silent.
The scientist came in close. "I am Dr. Kratkan. This is Commando Rugot. My dear Hunter, you have been in a coma for two weeks, but thanks to the Phazon infusion, you have recovered at a rate faster than we could have ever anticipated... By my calculations, you should be able to walk within the week. But no fighting. Yet."
Samus looked at Dr. Kratkan with wide eyes. Make that three anomalies - suit readings indicated Phazon levels of 80%, higher than it had been on Phaaze.
"But… Phazon…" Samus barely uttered the words before wincing at a sharp pain in her ribs. She glanced at her hand and noticed her skin was a faint shade of blue.
>Dr. Kratkan chuckled. "You didn't think that destroying Phaaze was enough, did you? Let me show you something." At the click of a button on his tablet, a monitor appeared in front of Samus' face. An image of a planet radiating a blue light was on the screen.
"That is Frazna, where we are currently. This is the last planet to have a Leviathan seed, producing Phazon as a living organism. Like Phaaze, Frazna is also sentient. It is the source of what you call Space Pirates, we call Fraznaor."
The monitor blinked to another slide. A Metroid.
"In the event of an emergency, we stored some Metroids here in order to preserve the species… As you know, on Tallon IV we were researching their life-force properties. We are on the brink of a solution.</p>
"I'm sure you're probably wondering why we spared you when we could have left you for dead. You see, Samus, you could be this universe's most powerful weapon, with the right training. And you could help us eliminate the Galactic Federation, with which I know you are not on exactly… friendly terms with."
He was right. The Galactic Federation would now want her for the "unlawful destruction" of their research, ready at any moment to wage war with her. There were many illegal weapons stored there, no longer accessible. Somebody had to pay for it - and a rogue bounty hunter was the ideal target.
Cmo. Rugot stepped in. "I'm sure you hate us to an unimaginable degree, but now we have something in common. We both now understand the evils of the Galactic Federation. And we want your help. Not like you have much of a say in the matter. If you try to flee, the Federation will be right there to capture you. And in your current state, I don't think you can put up a fight."
Go back to the Federation and face prison, flee helplessly from the Pirates while being critically injured, or stay, recover, and be made a leader amongst them? It was confusing, but the decision to stay felt right. There were no other options.
Chapter 2: Zero Mission
After a few days, Samus had been rehabilitated enough to walk slowly, with the help of a nurse. Thanks to the Phazon, the fractures in her legs and ribs healed entirely; now it was time to regenerate the atrophied muscle tissue. As time passed, Samus began to assume more and more the role of the Pirate leader.
One particular afternoon, just one week after waking, Samus was approached mid-physical therapy by Cmo. Prazo, her personal advisor.
"Samus, you seem to be doing much better."
"You're telling me." Samus chuckled, stretching out her left leg.
"Well, with that in mind, there's something I'd like to ask you."
"And what's that?" Now the right leg.
"We've received reports of Federation battle ships approaching the Yozar region approximately 50 lightyears away from here. While we are able to cloak Frazna with our Phazon technologies, we suspect that they are on the hunt for you. It will take them approximately one month to arrive near our location, and by then you should be in fit shape."
"What are you getting at, exactly, Commando?" Samus squinted her eyes.
"As you are our new leader, I would like you to spearhead the counter-assault against the Federation forces when they arrive."
A terrible feeling wrenched her gut. "Counter-assault?"
"Yes. We have some plans laid aside, but we wanted to run it by you first. You wouldn't be doing any fighting. Unless you want to."
She paused for a minute. "Cancel all of my plans, and announce a meeting to all Class 3 and up Commandos to take place in the war room in two hours. I'll be waiting."
Samus stood tall behind a podium as twenty Commandos of varying ranks - including Cmo. Rugot and Cmo. Prazo - sat around a table in front of her. A map of the Yozar region was projected in the middle of the room.
"As I have been informed, and you all probably know, Federation battle ships are approaching Frazna and will arrive in approximately thirty days. We anticipate that they will not be able to detect our exact location should we activate our cloaking devices, but this is the prime opportunity for our first strike.
"First, the 3rd Battalion led by Cmo. Tukla will hide in orbit of Hobak, while the 1st and 2nd Battalions will stay stationed in front of Frazna. As their battleships approaches Frazna, within 0.25 lightyears we will decloak and the 3rd Battalion will strike from behind.
"As their ships struggle with that Battalion, the 1st and 2nd will swoop in, board the ships, and take hostage the ships’ captains. Once that is completed, we will park their ships in a holding area to research any possible confidential information aboard. Are there any questions?"
Not a single Commando raised their hands. They all nodded in agreement. Samus did a half-smile.
"I thought so. For now, I will be in Research Lab Alpha."
Samus walked carefully from the war room to a main entrance which branched off in two directions. To the left were training facilities, and to the right the research sector where Science Team was located. As she walked right toward the research sector, she crossed glances with different Pirate Grunts who shirked away in fear.
At the gateway to the research sector, Samus entered into a purification chamber. A computerized voice rang from the intercom.
"Voice identification, please."
A panel dropped down from the ceiling.
"Please approach the ocular scanner."
A light scanned from left to right over her eyes.
"Welcome, Samus. Please activate your Varia Suit before continuing."
It'd been over a week since she'd donned the Varia Suit. It was time to see if she was ready for it.
Samus closed her eyes and pressed a button on her left wrist. A bright, yellow light eminated from her body as she floated up ever so slightly above the ground. The suit began appearing in fragments around her until she dropped back down to the ground. Opening her eyes, the purification chamber activated a vacuum to remove any contamination. Finally, the opposite door opened. She took one step forward and felt a weakness in her legs. The suit was heavier than she remembered.
An elevator greeted her just in front of the door.