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Alright, Let’s get on with it: Credit for this goes to Alphamon Burstmode X from fanfiction.net, go check him out.
There it was. The Baby. The Metroid that had bonded with Samus Aran on the planet sr388 and it had just been struck down by Mother Brain. Samus knelt down next to the dying Metroid as the glow that eminated from it slowly left. Samus began to silently weap next to the now dead creature before she looked at her arm canon which was now glowing in a rainbow.
"Mother!" Samus shouted before turning to the organic computer with hate filled eyes behind her visor. "Time to go." She said coldly before launching out the very same attack that Mother Brain had use to wound her earlier causing the AI to let out crys of agonizing pain with every single hit. After a few mear minutes of continued fire from the colorful rape beam, Mother Brain finaly fell to the ground before turning to dust and blowing away.
Samus then heard a loud alarm going off. Said alarm was the sound of self destruct the trigger of which was most likely triggered by the destruction of the AI. Samus then prepared to make a run for it to escape. However just before taking her first step, she heard crying coming from behind her. She then turned around and activated her echo visor to see where it was coming from and upon doing so, saw the sound waves of the crying coming the carcas of the Baby.
Samus then ran over to the Metroid just before the outer shell broke open to reveal a small female child that looked to be about 3 years old with pale green skin, short dark green hair blood red eye and if not for those features, looked like Samus when she was 3. The child was still crying while holding her arm which was clearly burned by a laser blast.
"Mommy. It hurts." The girl whispered as she looked up at Samus as the realization struck her like a truck to the face. Somehow the Baby Metroid had evloved in to a humanoid form. Just like when Metroid Prime had evolved in to Dark Samus.
Samus took a moment to compose her self before picking up the girl and wrapping her in a Space Pirate flag she ripped from a nearby wall. "Shh. It's okay. I'm here." She whipered as her helmet flashed off before she kissed the wound on the Human Metroid's arm.
"Self destruct in 3:00 minutes." A voice said on the speekers promting Samus reactivate her helmate and star running throught the coridors as fast as she could as the girl held on to her neck. After Samus rescued the animals from the cell they were in. It was smooth sailing back to the ship with 1:15 minutes to spare.
Upon getting a safe distance from Zebes, Samus looked back to see her childhood home expode along with what ever remained of Mother Brain and Ridley. Samus then looked down to the Human Metroid toddler that was now sleeping in her lap before a smile graced her lips. Just then the com on her ship chimed up.
"Samus Aron, come in. This is the star ship Dragoon. Please respond." The GF captain said.
"Samus here." She said in to the comunicator.
"It's good to here from you, ms. Aron" The Captain said. "What's your status." He asked while atempting to get a debrief of the mission.
"Planet Zebes has been completly destroyed along with the Space Pirates and Mother Brain." Samus explained to the Captain.
"What about the Metroid? The higher ups need to know what happened." The captain said as Samus looked down at the little girl in his lap.
"The Metroid was destroyed." She lyed knowing what awated the Metroid girl if the Federation knew about her. The experiments, the pain, and the strait up torture they would put her through in order for them to make her in to a weapon or worse. Make an entire army of Metroids and there was absolutely no way in the 7 Hells that Samus would ever let that happen.
"Understood. Do you require any medical assistence?" The Captain asked.
"That won't be necassery. Samus out." Our favorite Bounty Hunter said before she turned off the com. She then looked back to the child as yet another gentle graced her lips.
(Scene change: Undisclosed Planet. Population: 2)
After a few more hours of flight through space. Samus finaly reached her secret compound. (With all her enimies, she seems the type to have 1.) After letting out the animals she saved on Zebes in to the field on the east end of the compound, she carried the little girl inside and in to her bed room before lying down with the Metroid girl still in her arms. She then started to run her hand across the childs head.
"I promise, I will always be there to protect you... Virginia." She whipered in a soothing voice as she gave the girl a name. The name of her own mother. The woman who sacraficed her own life to protect Samus (Fitting considering how the Metroid had mere hours ago, almost done the same thing.) and the bounty hunter was more than certain that given the chance, she would do the very same for the girl in her arm. Her daughter.
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