Author's Note: Well, I hadn't been planning on writing another Metroid story so soon, but I've had this little plot bunny hopping around in my head for a while and really needed to start a new project. (Apologies to anyone who was hoping for more "Eevee Quest" instead. I'm having a bit of writer's block on that story.)

This story, as you may have already figured out, takes place after the events of Metroid Fusion. It is in the same AU as my other Metroid stories, but they are not required reading to understand this one. I do think that reading "Human" and "Spawn" will enhance your understanding of the world and characters, but they are also dramas and thus much slower than this story. While not required, I strongly recommend reading "Xenophobia" before reading this story. It's a Metroid/Aliens crossover, but knowledge of Aliens in not required to understand it. (Although Aliens is a great movies and I highly recommend it.) Of course, if you do read this story without reading the others, know that it contains spoilers for the others in the series.

Anyway, I've always wanted to do something post-Fusion with a fugitive Samus, so I'm looking forward to writing this story. Hope you enjoy! :)

Zero Host

Chapter 1: Rogue

Drops of red blood fell to the floor, burning superficial holes in the steel hull. The cargo bay was dark, titanium crates stacked halfway up to its massive ceiling, but its vast expanse left a lot of empty space. The low hum of the engines could be heard, though it was muffled by the thick steel walls. It had been closed up and locked hours ago as the ship's crew had retired for the simulated night aboard the transport craft. It would not be open again until they reached their destination.

Not so much as a rodent stirred anywhere within the pristine cargo hold, save for a small band of creatures in a dark corner far from the main doors. Hidden from the view of anyone who might enter, six entities stood behind a row of the massive transport crates. Three blue, tailless primates looked curiously out into the rest of the bay. Their ears looked too large on their small bodies but were particularly sensitive to sounds, and they listened intently for any sounds coming from elsewhere on the ship. For the moment, all was quiet.

Hidden further in the shadows was a large, green bird-like creature with sharp red eyes. Its legs were long and powerful, although its small wings suggested it lacked the ability to fly. A chick of the same species stood at its feet as the intelligent-looking bird stood watch over its young and the final member of their group. Up against the wall sat a heavily armored humanoid figure. Its body was concealed beneath a yellow armor that appeared to have an orange layer of organic armor covering vast stretches of its limbs and breastplate. Below the right elbow, there was a long green cannon in place of an arm, and on its other half, razor sharp spikes protruded from its forearm. At the moment, the humanoid was not wearing a helmet, revealing the mostly-human looking face of a woman.

Her long blonde hair was tied back in a messy, high ponytail caked with sweat. Black vein-like lines traveled down the right side of her face, giving her blue-green eyes an other worldly look. As she raised her armored palm up to her face, she spat into it and pulled it away to see dark blood mixed with her saliva. Disgusted, she let it drip to the ground where it burned through the top layer as though it were strongly acidic. The woman did not seem at all surprised by this. She was used to it.

The tall green bird looked at her with concern, its feathery green mohawk giving it an almost comical look.

"I'm fine," the woman said in a deep voice, looking up at the avian alien.

The bird continued to stare at her skeptically, as though to say that if the woman were truly fine, she would not be spitting out blood.

"Seriously," the woman said with more force as she glared at her companion. She was well versed in communicating with avian species, even if this creature, a dachora, was not the type with whom she normally spoke. "My armor is done repairing itself, and my body heals quickly."

At least, her body always had healed quickly in the past. As she ran her tongue over her teeth, she noted for the thousandth time that she now possessed long fangs where her eyeteeth had been, yet another side effect of her latest mutation. Holding up her left hand again, she stared at its sharp forearm protrusions with the same disinterested disgust with which she had earlier regarded her own spit. A quick glance over the rest of her body did not seem to improve her mood at all as she leaned back more heavily against the wall and sighed.

The woman, Samus Aran, was a mercenary. At least, she had been a mercenary until the incident that had landed her in this situation. Most of her career had been fairly straight forward, either protecting things or shooting things and occasionally doing both simultaneously. That was a vast oversimplification of what her jobs had entailed over the years, but in retrospect, most had not involved the difficult sort of moral quandaries with which she had found herself struggling on her last mission. Although, on some level she was not surprised to find herself where she was now. Since the end of the Space Pirate War almost five years ago, the general climate of the Galactic Federation and its territories had been changing, and she had long since suspected they were no longer the entity she had once fought to preserve.

This last mission though, the one that had landed her in this mess, had been so stupidly simple it boggled her mind to think just how ridiculously out of control everything had spiraled. She had contracted with an employer with whom she had contracted dozens of times in the past, a company called Biologic. All she was supposed to do this time around was lead a few scientists around the remains of SR-388, a planet she had cleared of a Metroid infestation five years back, and cover them while they collected flora and fauna samples to bring back to the space labs they were building.

She cursed herself for being so careless as to let one of the native creatures, a gelatinous parasite referred to as "X" infect her and not doing anything to address the situation until she fell unconscious and had to be ejected from her ship as it veered off course and exploded as it crashed into an asteroid. While it had not been her only ship, it had been her favorite and the one she had owned the longest, but the loss of her ship had not been the worst part of the ordeal. As the parasite spread through her body, she was rescued by a team of Federation scientists who had taken her straight into an emergency surgery in an attempt to save her life.

Of course, her powersuit was fully integrated with her central nervous system, and there was no way for anyone to remove it while she was unconscious, so they had cut into the armor, removing whole large sections of it. Supposedly, they had done it because they thought it would save her, but the mercenary had her doubts. At some point, someone had just so happened to suggest injecting her with a vaccine made from the cells of the last Metroid, a specimen Samus herself had delivered to the Federation Ceres Station toward the end of the Space Pirate War. It was news to her that any cells from the creature still existed, having been assured long ago that all Metroid samples had been lost in the attack on the Ceres Station and no further research could be done with Metroid cells.

If course, she had not asked any questions about that when the vaccine made from the Metroid DNA had "miraculously" saved her life, restoring her to full consciousness as an organic blue layer grew over the sections of her armor that had been forcibly removed. She was not sure what the new blue outer layer had been, although it felt, in a way, like it was the suit itself scarring over rapidly in an attempt to protect its vulnerable areas. Whatever it was, it left her armor with a drastically different appearance, and given that the armor was essentially a part of her body, she loathed wondering if her humanoid body within it had also been drastically altered.

That was no miracle, she thought bitterly as she coughed and spat more blood into her palm. They set me up. They knew about the X all along and had the Metroid vaccine ready as soon as I got there. Pretending to save my life was just an excuse for them to cripple my defense systems.

Indeed, despite the new organic layer, the surgery had left the mercenary severely weakened and nearly defenseless against the creatures she had been dispatched to fight soon after awakening. They had the audacity to send her onboard the Biologic Space Labs to try to save it from falling to the X infestation they had "unwittingly" brought aboard when they sent over the discarded portions of her suit for research, pieces of her suit they had cut away and taken without her knowledge or permission. Given that the X had the power to mimic their deceased hosts, she knew exactly what they were trying to create using the parts of her suit, but they had definitely gotten more than they bargained for, and that creature had busted out of their quarantine bay without any effort at all.

The SA-X. Just thinking about that creature made Samus's blood run cold, even now that she knew all remaining specimens had been blasted to bits when she had sent the BSL on a collision course to planet SR-388, destroying both the station and the planet in the process. While it had wiped out the X parasite species, it also destroyed anything that might have escaped the bioweapons experiment labs she had discovered on the BSL. She was not sure if they fully realized the irony of that situation, how they had tricked her into the mission on the BSL in order to stop the SA-X from destroying their cloned Metroids, the very same species she had personally exterminated. And when that had failed, their efforts had shifted to an even greater prize: capturing the SA-X.

The sour acidity of her blood filled her mouth as she thought about that creature, the SA-X with its dead eyes as it had stared at her, hunting her down like a dog as she had been forced to hide repeatedly in its presence. Too weak from her near death at the mercy of the X infection, she had not even had the ability to scratch the SA-X for most of the BSL mission. Because it was her. An X clone of Samus herself at full power, and its power was terrifying. Even still, she had not uttered a word of complaint at having to carry on the mission despite its presence because she had honestly believed she was there to rescue survivors. But the ultimate betrayal had come when she learned that the Federation had intentionally withheld weapons from her that would have given her the ability to fight it, choosing instead to keep her weak so that they might attempt to capture and use the SA-X without her being able to destroy it or oppose them.

Learning how the Federation had turned on her and used her as a pawn had stung more than any wound she had been dealt in that battle, and at the end of it all, she had hit them back ten-fold, going rogue and completely annihilating both their prized bioweapons and the planet from which they had harvested them. And that was why she now found herself as a fugitive hiding out in the cargo bay of an illegal transport vessel.

There were, however, a few good things that had come out of her mission on the BSL, she thought as she looked around at the dachoras and little blue etecoons. Had she not rescued them from the labs, the intelligent creatures also would have fallen prey to the X, and having them with her now was the one tiny grain of solace she could find in this disaster. Although there was, perhaps, one other good thing that had come out of it.

Wiping any remaining acidic blood on her breastplate, she reached beside her and picked up a compact, metallic cylinder. It was only a few centimeters thick and so small it fit in the palm of her hand. At the center was a red light, but it was dark for the moment. She had switched it off a while back, needing to clear her thoughts before dealing with what was inside of the device.

Adam Malkovich, her former Commanding Officer and longtime friend. Apparently, the Federation had made a habit of uploading the minds of their military leaders and scientists so that they could still utilize them in the event of their deaths. The thought was sickening and bizarre, and as happy as she had been to be reunited with Adam's mind, it confused her in a lot of ways. It had been years since she had heard her late friend's voice, and discovering his mind lived within the programing of her computerized CO had been like seeing a ghost. And she was not so sure it was a good thing.

While she had her concerns about the Adam program, she had made sure to download it to the compact device she now held before detonating the explosives on the ship she had stolen from the Federation and making a run for it out into Deep Space. Now that she had a few moments of quiet, she figured it was a better time to reflect on how their reunion had come to be, specifically why, out of all the AI systems the Federation could have programmed to be her CO on this mission, they had chosen the one programmed from a person she had actually known in life.

Samus wanted to find the answers to those questions, but they eluded her for the moment as a wave of exhaustion rolled over her and she yawned, exposing her new fangs to the dachora whose red eyes grew wide in surprise.

"Sorry," the mercenary said with a grunt. "Didn't mean to startle you."

She wondered how long these aliens would be her companions now that she found herself on the other side of the law. A former fugitive recovery agent herself, she knew better than anyone else that the bounty hunters of the galaxy were already hot on her trail and anyone she came into contact with was a potential target. But better than anyone else, she also knew how intergalactic bounty hunters operated, and they were going to be in for one hell of a fight if they thought they would be able to apprehend Samus Aran.

Bounty hunters and military manhunts didn't frighten her. She'd stared down death too many times in the past, and with her years of training and experience, she had little doubt in her ability not only to stay out of their grasp, but to find ways to live almost comfortably while doing so. Only one thing gave her pause.

While she had been well known as the most powerful and accomplished bounty hunter in the galaxy during the Space Pirate War, that had been a long time ago now. For the past four and a half years, she had been living an almost quiet life on a planet called Earth. And while it didn't bother her to leave the planet behind, she knew she was not quite the free agent she had once been. Somewhere on that planet, her loving partner and her son were learning of her disappearance and her shift from the most feared warrior in the galaxy to the most wanted criminal in the galaxy. And she was not naïve enough to think that her enemies in the Federation would not find a way to use them against her.

As tempting as it was to blow off the Federation and build a life for herself outside their borders, she knew it was not an option now. Their officials may have stabbed her in the back, but there were still innocent people living within Federation territory, people had once dedicated her life to protecting. And now they included her own small family on Earth.

Even if the Federation didn't go after her family to try to get to her, Samus knew they were not safe. No one was safe now that the Galactic Federation itself was backing bioweapons research and construction. If they would go so far as to revive the Metroids, once believed to be the most dangerous species in the galaxy, there was no telling what other sort of sick experiments they had planned. And it would not be long before they created something they would not be able to control.