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Metroid: Annihilation takes place after the real game Metroid Fusion.
Thus, it chronologically takes place after all of the Metroid games.
Text written in blue is notes to the reader(s)although there is none.
In progress.

Intro: After CorruptionEdit

Destruction. Everywhere. My instinct is to escape. To survive. Now laying on the deck in the single room of the starship, Dark Samus reflected on what had happened. After taking substantial damage from her Genetic Host Samus, she merged into her AU she had took from the Galactic Federation. It was her instinct to survive. However, Samus outdid even her AU, and in the destruction fled to a nearby chamber where a special type of Phazon was being produced by the planet.

Phazon was sentient and alive, {It really is; this can be seen in Prime 3} but was such a malevolent force that it required a telepathic link with a massive force to keep it sane. Without this force, it literally destroys itself. Thus, should the planet Phaaze be destroyed, all Phazon would die. But this type was made not too. It was just like the kind Dark Samus herself was made of. Should Phaaze be destroyed, this would be her final resort to survive. However, the moment Phaaze was destroyed, the starship would start to die.

As the ship drifted among the debris of Phaaze, it recognized Samus' starship and, after a mental confirmation from Dark Samus, drifted to where the ship was. Samus had already jumped from space, and Dark Samus' ship picked up on its trail, something no mechanical starship could accomplish. She would follow Samus, learn where she was going and plan from there.

Pre-Metroid: 1,006,239 years backEdit

They were a strong race known as the Space Pirates. They possessed powerful warriors, and intelligent scientists. They had no interests in befriending other races. Others were meant to be conquered. One of the many 'odd' (as considered by other races of creatures) was how the Space Pirates treated their society. One aspect was how they dealt with defects. Space Pirates received tests at birth; should they have mental defects or a disease, they would be dealt with. Those with diseases or those that were paralyzed were put into the scientific industry. If they couldn't fulfill anything there or didn't have promise, they were dealt with the same way those with mental defects were treated: they were executed.

Originally they were ejected into space, however, when the Space Pirates achieved space travel and exploration, the bodies became a problem. Starships would often collide with them, and, moving faster than the speed of light, would cause the ship to be torn apart, wasting resources. So they then found a planet. At first they had sent several probes down to the planet, but they all disappeared when they reached the it's atmosphere. It appeared highly corrosive, and they couldn't make anything to withstand it. So they would simply get a ship close enough to the planet's gravity, and eject the defected Pirates. They would be drawn to the planet, and fall to it like meteorites. This served the Pirates perfectly. Because of its use, they called it Executous.

However, it wasn't just defected Pirates. Those that died from natural causes, such as old age, were also taken to Executuos. And there was still more. There was defected Pirates who didn't become defected naturally. It was no secret that the Space Pirates constantly experimented upon themselves {This part is true; you'll know if you've played Prime 1 or 3}, and failures were always happening. Pirates that had work done upon them and proved unusable or not of interest were also executed, just like the others. Punishment among Pirates was strict, and a mere crime could earn the same treatment as the previously mentioned Pirates.

However, it wasn't long before strange phenomenons were noticed by Executous. Many soon called it and the space around it cursed. Starships would go missing, and few came back. Those that did drift back had no living crew. The members of the ships had either killed themselves or murdered each other. All electronics aboard the ships were corroded. At first they believed it was all a staging, and other races were doing it. After all, they were Pirates and plundered others, making virtually every other race their enemies. However, it was revealed something much more sinister was at work when they built an expensive state-of-the-art probe that beamed back real-time images to their HQ.

The probe followed behind one of their cargo ships that was heading by the planet, and as they watched in bafflement and horror, chaos ensued. At first the ship stopped, and all engines aboard the ship failed. The probe instantly gained static, but it's relays withstood whatever was trying to disable it. The crew aboard the ship dropped to the floor clutching their heads, unknowing what was going on. After a few minutes they all tackled each other, their eyes blazing with insanity. When only one was left, he proceeded to beat his head off of a wall until he succumbed to blunt force trauma. In a few moments the probe had withstood all it could take, and the HQ stopped receiving images immediately after.

Intro: After Corruption - continuedEdit

As Samus dropped into space, her alarms instantly notified her of a strange object. However, as she looked at her radar, it disappeared. It was most likely a passing comet. She landed on the planet and exited her spaceship. She dropped to the landing platform and watched the sunset, reflecting on what had just happened in the past week {This pretty much does occur in the 100% Item completion-ending of Prime 3}. She let her suit fade off and then entered her ship, unsure of where to go next.

FusionEdit

The events of the real-life game Metroid Fusion occur.

After FusionEdit

As her new spaceship soared through space, she couldn't help but feel awestruck by what happened. The Galactic Federation had been cloning Metroids. Again. This problem had previously occurred on The Bottleship, another of the Federation's secret activities that she uncovered. This time she truly hoped the Metroid threat was gone. She still felt the void in her heart though for her lost friend, the Baby Metroid. She had took it as her own child, and it had an affection for her too. Seeing the Metroids on the B.S.L. Research Station and having to fight them ... just knowing each was a genetic replica of her Baby Metroid.

As for the galaxy, it should be at peace now. The Metroids were extinct. The Space Pirates were wiped out. The source of all Phazon was destroyed. What was left? She had a question that continuously bothered her, and longed to ask Adam, but knew she couldn't. 'Was there more secret projects the Federation was conducting?'. Even if he wanted to tell her, he most likely wouldn't be allowed. And, even more fearsome, if there was some even he didn't know about. Deep in thought, she drifted asleep, weary from the hard work at the B.S.L. Station.

Pre-Metroid: 3,000 years backEdit

Space Pirate - Planet Valark Log; Day 23

As the leader of the forces of the Space Pirates on their newly discovered planet, which they named Valark, Taknar could only think of one thing. The birds. He was a general in the Pirate's armies, and had led planet-conquering battles before. But this race, which called themselves the Chozo, were highly advanced. This planet had vast resources, and could serve as a great place to set up an HQ to plan other planet assaults. But these creatures didn't want to let them have it. It first started when their scouting party of troops didn't come back. Knowing that something attacked them, they sent him to lead five platoons of their finest troops.

Currently, the losses were mounting. Platoon 1 had only three of originally twenty troops left, and the other Platoons had lost at least a fourth of their fighters. Despite the Pirates having ranged energy-beam weapons and the Chozo having mere spears and other melee weapons, the odds for the Pirates weren't good. They were fighting on the Chozo's territory, giving them an advantage over navigating the terrain. Second, the Chozo warriors were not only amazing fighters, but also masters of stealth.

So, in retaliation, we are making our own warriors. The project has been dubbed "Operation: Valark Warriors". Back at our homeworld, Urtraghus {Which it really is named in the Japanese version of Prime 3}, we are taking our most athletic and cunning warriors, giving them special steroids to further boost muscle mass, and training them in the arts of melee warriors.

Space Pirate - Planet Valark Log; Day 34

All of our attempts to capture a live Chozo warrior have been unsuccessful. Today we managed to sedate one at the expense of four of our troops, but it soon regained consciousness en route to our lab. From what the troops report, it tore the binding of it's left arm and slit it's throat with it's claws, immediately dieing. Sadly, I had to contact HQ and request another three platoons of troops as well today. These, along with the remnants of what was the original five Platoons, are all I have until Operation: Valark Warriors is perfected and arrives. HQ is also getting impatient of having no live Chozo to work with.

However, we were still able to extract multiple samples of DNA and Genetic Information from the body, and sent it back to HQ for 'something special' they are planning.

Space Pirate - Planet Valark Log; Day 42

This isn't going well. Last night the Chozo raided our base, torching our main supply of rations and sabotaging two of our generators before we fought them off. They didn't come for battle, though, and luckily there was no causalities. However, all Pirates are now eating 60% less than what they should be, and I dare not tell HQ we need more rations, or they will surely have me demoted from General to Soldier; and that is considering if I am lucky.

HQ just got back: they say they have infused their warriors with the Chozo DNA, and are commencing the final experiment tests. If all goes well, we will get our warriors in about two weeks.

After Fusion; Dark SamusEdit

It was the ultimate army. Thousands of Phazon-enhanced Space Pirates lay before them, hibernating, awaiting their wake-up call for battle. And it was all hers. Sort of. She remembered back to what had happened: after following Samus to a planet, she realized she would need something stronger to destroy her - she herself was too weak to defeat Samus in a one-on-one battle. Instead, she need a planet to host her Phazon, before her ship died. Traveling through system after system, she scouted each planet from space, trying to find one that didn't have some sort of military force. But then she was attacked.

Her ship suddenly came to a stop, and started shaking in uncontrollable spasms. She herself felt it too - something was pounding her brain, an unbelievably intense force she couldn't understand. And then it stopped. He ship was being pulled towards a planet, which appeared to be plagued with a corrosive atmosphere. But then the clouds of acid parted, some force at work. Her ship soon landed, and she found herself in front of some sort of vast temple. Something was trying to communicate with her. She opened her mind, allowing any thoughts to become hers. It was some sort of creature deep within the temple, calling to her. She followed it, and after some navigating through the ancient building, found a massive creature before her. It was large and green, had two tentacles, and contained an eye within a razor-sharp tooth filled mouth. Communicating telepathically, they made a deal.

She called the creature Phantoon {Super Metroid/Other M, anyone?}. Apparently, it was part of two dimensions: the living, and the spiritual. It had amassed an army of Space Pirates, all from the Space Pirates themselves. To prevent the bodies from burning up from the travel through atmosphere or the acid, Phantoon would open a void, allowing the body through unscathed. They were, however, already dead: from being jettisoned in space, they had instantly froze to death from the vacuum of space, obviously. Phantoon could also alter the entire planet's gravity (or sections of it too) to slow the decent of the bodies, so that they didn't impact the ground and splatter for a mile everywhere.

He'd then pull their spirits from the afterlife, resealing them back in their bodies. Knowing that they had been betrayed by their own brothers, the Pirates were filled with hatred and a desire for revenge. Phantoon would then put them into a deep hibernation. Over the centuries, he had amassed an army of Pirates. And then Dark Samus showed up. Together, they had to trust each other. Without Phantoon, Samus' ship would die, and there would be no hope for her to spread Phazon. Without Dark Samus, Phantoon just had an army of unarmed pirates.

By working together, Phantoon now hosted Samus' Phazon, serving as the host in the place of Phaaze, also dispersing it across the planet. He now had an army of Phazon-modified Pirates, making his force much stronger. And these weren't like the Phazon-modified troops the other Space Pirates had. These were modified using the same Black Phazon Dark Samus was composed of, making them stronger beyond anything the standard blue Phazon could do. The same went for the planet, it was now even superior to Phaaze, being composed of Black Phazon.

Pre-Metroid: 3,000 years backEdit

Space Pirate - Planet Valark Log; Day 59

Operation Valark Warrior

A 'Valark Warrior'

Off by a few days, our new warriors have arrived today, along with a large shipment of rations and some new equipment. Currently, our standard troops come with an arm-cannon and an energy scythe, each on a different arm. These new ones have scythes on both arms, which are a new, much more powerful experimental type.

Space Pirate - Planet Valark Log; Day 62

These Valark Warriors are a blessing. Just today we had four troops scouting the area with the protection of three Valark Warriors. A group of eight Chozo warriors ambushed them. No Chozo survived. Normally, that many Chozo would have annihilated at least an entire platoon - we've never encountered a group of that size before, but our Warriors handled them with ease. They are surprisingly agile, able to scale cliffs faster than my best scouts could have imagined.

But their is cons. These new Pirates are very aggressive, even by our standards, and won't hesitate to chop whatever bothers them in half. The leader from Platoon 2 made the mistake of agitating one of the Valark Warriors, and when we found him, he was basically in pieces. For safety, we secretly lock their living quarters shut when we sleep, but they don't need to know that.

Space Pirate - Planet Valark Log; Day 67

We have discovered what appears to be a Chozo village. It won't be no easy task though, our scouts reported a sighted twenty three Chozo warriors. Seeing that we have ten Valark Warriors, we are currently debating when to strike. We need to have the way cleared in three days, which is when our HQ will send more materials to expand this lab into another HQ, and we can't have enemies lurking nearby. An air strike might work, if it wasn't that the village was in a cavern.

It has been decided. We will storm the village tomorrow, when they send a group of their warriors on a hunt. They, from what our scouts report, send two groups of three warriors out at around mid-day to hunt. We will send all of our Valark warriors, and wipe out the village.

Space Pirate - Planet Valark Log; Day 68

As we follow behind the Valark Warriors, I try to hide the shaking of my arm. I'm not sure whether it's fear or excitement that makes me quiver right now. But I know all the troops feel the same way. There - we are here. We now wait for the hunting parties to leave. We pass the time counting warriors and villages, and plotting which angle to storm from. And now the first group left, then the second. Roughly, there should be seventeen warriors left.

Taknar sweeps his hand in an angle - the signal. The Valark Warriors jump from their position and charged forward, leaping to the walls and climbing, the platoon troops in follow. As the Warriors reach the top, they scream their deep guttural cries and leap into the village. By the time Taknar reaches the top of the wall, the scene below is a bloodbath: The Valark Warriors are slaughtering everything in sight, and he can't believe their performance. Villagers run in terror, but no mercy is shown. His troops reach the top of the wall with him, and they shoot anything that moves, picking off escaping villagers. In about three minutes the village is strewn with bodies, the warriors are just as easily killed in the chaos. The troops torch all the buildings, rooting out any survivors along the way. They then climb out of the village and leave, as if nothing had happened.

Space Pirate - Planet Valark Log; Day 70

We are already working on the HQ, and soon will get airships in here to wipe out other villages. We even received a compliment of thirty troops to aid in the protection of it. This is indeed a great time for the Space Pirates. In fact, we wil-what is that? Oh d- "It's an army!" I yell in our tongue, and scramble for the nearest assault rifle I can find.

As the Pirate Troops looked out, a swarm of what was at least forty Chozo scattered towards the HQ. They grabbed their rifles, and all ten Valark Warriors charged to meet the warriors. What appeared to be the leader - a Chozo bearing gold-colored armor - screeched the war cry of his troops. And then the unthinkable happened. The Valark Warriors turned - and charged the HQ. Both the Pirates and Chozo pause for a brief four second - unsure of what was happening. But then they realized: the Valark Warriors weren't the Pirate's allies. The Valark Warriors leaped upon what was just their comrades, hacking them all apart. The Chozo took this opportunity to charge the rest of the troops, barbaric with revenge.

Taknar shot every Chozo he saw, but they were too fast; only two shots found their mark, but they didn't even pierce the armor. As he fell back into the HQ with about twelve other troops, he slammed the lock on the main door, and it sealed shut. In horror they saw the rest of the unfortunate troops get picked off, one-by-one. And then I realized why this happened. The Valark Warriors had Chozo DNA. What was supposed to make them the ultimate fighter made them their enemies. They must have succumbed to the call of their nature to help their allies. They may have been Pirates, but their true Genetics were mostly Chozo. The Chozo retreated, but the Valark Warrior's didn't. Instead, they clawed at the windows, an awful sound of metal scraping crystal filling the air.

And then it happened: being the HQ was newly built, hardly anything was reinforced and inspected - one of the windows gave way. The Valknar Warriors filled the room, and all the Pirates could do was run. The Warriors, being much more agile, pursued them down the corridors, showing no mercy to their once-friends. He shot the one, determined to take at least one with him; but the beams didn't affect it. As the fourth one charged him, he swung his scythe and assault rifle, using the latter as a primitive club. But they were worthless against the Warrior. His left scythe caught Taknar's scythe, and with his right sheared the assault rifle into two halves. He then flicked his right scythe into Takner's and used the left to impale him. He felt weary - everything became foggy, and felt the last bit of life disappear as he felt his legs separate from his body in one swift swing from the Warrior's right scythe.

2 Months after FusionEdit

Startled awake by the still unfamiliar alert signal that indicated her ship was approaching it's destination, Samus quickly brushed over the screens in her ship, asserting everything was in no need of attention. Just then her monitor beeped, indicating it had an incoming message. She checked where it's coordinates originated from and, seeing it was from the Galactic Federation, opened the channel, and heard the unforgettable voice of Adam Malkovich. "Samus," he said briskly, "We need your help. The Space Pirates are back."

After a pause, she responded "The...Pirates? How?". His voice sounded nervous - something she never had heard in him before. "We don't know yet, but it appears they have a secret facility. Remember back to the Leviathan we used to warp to Phaaze? They somehow used one or something like it to reach and build a station in a far-away system. A distress-call probe drifted into a nearby Federation system, and appears to have been sent at least a year ago. It was meant for the Pirate Homeworld, but, being under our control now, we got it. Are you up for it?" She took all of this information in, and then responded "Yes. I'll go.". She heard his voice brighten. "I knew we could count on you. We have assembled another group of Bounty Hunters, as well as a fleet and army of our forces."

"Wait..." she said, realizing something was wrong with the story. "How will we get there?". He didn't respond for a few moments, and then said "While taking the Leviathan to Phaaze, we preserved Genetic samples of it. We then made an organic replica, and implemented into one of our ships. A cyborg version, if you will." She paused, not liking the sound of it. "When was this?", she asked curiously. "At the time of the Bottleship. It was another of the projects there. Upon blowing it up, though, we relocated the Leviathan clone. We now have recently awoke it from a hibernation it was put in, for safety reason. Any objections, Lady?" he asked, his friendly way of asserting their friendship. She held out a thumbs-down, smiling. As she looked out the view-port of her ship, she saw the GF Ship she was to board, identified as the 'G.F.S. Havoc'.

Upon exiting the ship, she was greeted by a GF Trooper, who gave her the coordinates of the ship. According to the map, all of the other Bounty Hunters were in a south section of the ship, in a room called the Mess Hall.

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