Rather than Kushina, Naruto's actual mother was an infamous intergalactic bounty hunter with an enormous body count to her name.
Known as Samus Aran, her ship crashed near the heart of fire country and was damaged beyond repair. With no ship and no operating distress beacon, Samus was left with no choice but to stay on the planet.
She was discovered by Minato Namikaze while he was on patrol, and after a short, but ridiculously destructive fight in which he only beats her after she runs low on energy, Samus explains her situation to him. Responding with his usual brand of kindness, Minato invites her to stay in the Konoha.
Two years before the Third Shinobi War, Samus finished a project to create a more streamlined version of her power suit. Utilizing the few intact systems in the wreckage of her ship, she integrated specially treated chakra metal into her normal suit, as well as creating a more compact version for stealth missions.
During the Third Shinobi War, Samus earned the title of the Leaf Village's "Armored Death*" for the raw number of enemy fatalities she was responsible for.
Afterwards, she and Minato begin a relationship and are soon secretly married. Samus soon becomes pregnant.
Due to the stress from the nine-tailed fox's attack, Samus goes into labor early. After giving birth to a baby boy, whom she names Naruto, she realizes that she is dying and leaves him a will of sorts for when he discovers her old workshop.
Either before he graduates from the Academy, or while he is training for the third stage of the Chunin Exam, Naruto stumbles upon the workshop and his dormant Chozo DNA causes the systems to activate.
After seeing his Mother's will, Naruto accepts his heritage and follows instructions that activate his dormant Chozo-born abilities, as well as allowing him to utilize the power suit.
Naruto Aran Uzumaki comes to the Third Exam and shocks everyone by attacking Neji with the Energy Cannon.
This story will be a small harem-fic. If I'm feeling particularly adventurous, I may add that glowing alien woman from Metroid Prime 3, or at least a relative of hers.
The Metroids will appear in this story (because anything Metroid-related isn't complete without them) in two ways. First, I'm having Naruto inherit Metroid DNA from Samus; I haven't decided on what abilities this will give him beyond some sort of sensor ability. Second, the strangely adorable and creepily endearing super-predators will appear in the Elemental Countries as well. For this part, I'm trying to decide whether to make a Metroid summoning contract, or have them simply appear as unaligned predators. Regardless of what I decide, there will be one Metroid that will fulfill the role of "Baby" for Naruto, and help him in combat, as well as daily interactions (before anyone asks; yes, I am using "Baby the Second**" for a "Kawaii!" element.) I'm looking forward to how I may be able to combine the abilities in combat.
I intend for Naruto's version of the power suit to look almost exactly like the Fusion Suit from Metroid Fusion. My reason for this is because of its organic appearance and the fact that it seems like it would work better for stealth.
Well, what do you guys think? I'd like some feedback and ideas while I flesh out more details.
*=I'm taking suggestions on better nicknames.
**= This is not going to be the Metroid's actual name.
*Preview of Neji/Naruto Fight*
The two combatants face each other in the center of the arena, one wearing white clothes with long, black hair and pure white eyes, the other wears a large brown cloak that hides his entire body from view, only the bottom of his whiskered face and a lock of spiky blonde hair showing beneath the hood.
The match starts, and the blonde makes the first move, his left arm flashing out of his cloak and launching three kunai at his opponent, who pulls out his own kunai and blocks with contemptible ease. So arrogant is he that he doesn't notice the fourth kunai that lands at his feet until he hears the attached tag begin to burn out.
He jumps to avoid the explosion only to lose a large chunk of his hair when a ball of super-heated plasma shoots by, narrowly missing his face.
Looking back at the blonde as he lands, Neji's eyes widen when he sees what appears to be a pine-green cylinder aimed at him, the opening in front glowing with another burst of barely restrained energy. Following the cylinder down its length, he sees it is attached to his opponent's right arm about an inch-and-a-half below the elbow, the rest of the exposed arm seems to be covered in some sort of skin-tight orange bodysuit.
Pulling his hood back to show his face, the blonde smirks confidently behind the green visor covering his eyes. In a voice bursting with quiet confidence, he speaks, "Hey there, I'm Naruto Aran. And you're my new target; so start running bitch-boy."
This said Naruto fires the shot, his arm snapping back from the recoil, and watches as Neji barely manages to dodge it.
This is gonna be fun.