It was the evening of the Tenth of October; ten years after a sudden and devastating attack of the Kyuubi no Kitsune, the strongest of the Great Tailed Beasts, on the Village of Konoha. The Fourth Hokage, Minato Namikaze, seeing no alternative, sealed the demon inside his newborn son, Naruto Uzumaki Namikaze, not that anyone knew of the fact. In fact, if they had been informed that Naruto was the son of their hero, perhaps they would have treated him with some kindness. As it was, however, he was hated and scorned by most of the adult civilians of the Village, and, because of a law made by the Third Hokage shortly upon retaking office, he didn't even know why.
Naruto groggily opened his eyes, weakly noting he was in some kind of giant tube, surrounded by a liquid. Although he could just barely see two men in front of the glass, he could hear them quite well.
"What is the status of the Jinchuuriki?" An older voice asked.
"He is currently stable, Lord Danzo. We were able to secure him with little difficulty, and are ready to begin the process." Another, younger voice said.
"Excellent, excellent." The one named Danzo almost sounded giddy. "We must hurry; the old fool will soon finish the work I buried him under and start searching for it. Start the process immediately."
"As you command, Lord Danzo." The second man pressed some buttons and Naruto fell into unconsciousness.
Danzo was happier now that he ever remembered. Tonight he would finally accomplish his goals of turning the Kyuubi brat into a powerful weapon, despite constant interference from the Third Hokage. The only real problem he had was figuring what the four little metal slabs he found in a very old laboratory under the village were for. He was certain they were some form of weapon, he had found many references to them from what little he could understand of the reports in the ancient room. For instance, he had found out they were so called implants, which would enhance some human aspects. He decided to use the Kyuubi boy because of his abnormal healing. After brainwashing, the brat would make an invaluable weapon.
After many hours of very dangerous surgery and repeated cutting open the back of Naruto's head, all four implants had been inserted into his brain and somehow, through the combined use of jutsu and technology, wired in with it; Naruto was returned to the vat shortly.
Mindscape, after surgery
Naruto was really confused right about now. He woke up in a big empty field, that was black for some reason, and was immediately surrounded by four figures. Figures that had blue skin and white hair and eyes, wearing green pants and black boots, and nothing else. All four had quite a lot muscles, and even some scars. After a few minutes of confirming that they weren't actually attacking him, he looked at the one in front of him.
"Where am I?"
"In your mind, apparently." The man shrugged.
"Great." Naruto sweat dropped, looking around. "Who are you? And how did you get in here, anyway."
"We're GI. Genetic Infantry." He elaborated at Naruto's look. "We're special soldiers from a long time ago that were made to win wars or die so humans don't have to. My name is Rouge. To my left are Gunnar," The man, who looked like he was younger than the rest, waved at Naruto. "Helm" The next one nodded with a kind smile. "And Bagman." The last one grumbled a 'hello'. "Ignore him, he's always like that." Bagman shot a glare at Rouge but said nothing. Rouge then told Naruto of the history of Nu Earth and creation of the GIs (: Which I don't know because I only played the game, and even then I paid little mind to the story. I just shot things.:)
"The reason we're here." Helm continued. "Is because GIs can survive in the form of special chips called 'implants' or chips, even a very long period of time, if done correctly."
"We're the last, apparently." Bagman said with a frown. "We have some idea of what's going on on the outside. The man behind this whole mess found a hidden cache of GI chips in an abandoned facility. He killed several good men because he took their chips out of cryo-chambers."
"Very cold rooms." Helm elaborated at Naruto's look.
"Yeah, we were very luck he learned how to handle chips when he stumbled on us." Gunnar added.
"Wait, how did I even get here in the first place?"
"Some men kidnaped you and shoved our chips in your head." Gunnar said.
"Well, it's a little more complicated than that, but that's basically the gist of it." Helm added.
"And now they plan to brainwash you and turn you into their puppet."
"What! Hell no!"
"Watch your language." Helm admonished him.
"Anyway, we thought you wouldn't like that, so we've been counteracting the chemical process." Rogue said, drawing a grateful smile from the young blond "And while we wait for some help from outside, the four of us will slowly begin transferring our skills and knowledge to you."
"However, you will probably end up in a coma for several years." Helm added as an afterthought.
"Alright, let's do it." Naruto said after a few seconds of thought.
"Lord Danzo, the process is almost finished." One of Danzo's personal Root Anbu informed him.
"Excellent, prepare the-" He was cut off by a big boom coming from behind them and a door opening to show an ou-of-breath Root Anbu.
"Lord Danzo, the-" A blade suddenly ended up embedded in his chest and he fell down, dead. The doorway revealed another Anbu, only this one had a mask painted to look like a hawk, unlike the Root's blank masks.
"Hello there." HE said, moving inside to allow more Anbu to enter, followed by a very pissed-off-looking Hokage.
"Just what the hell do you think you're doing with Naruto, Danzo?" The old man growled out with a murderous look in his eyes, scaring the one-armed man.
"Sarutobi, please listen to me. I-"
"Shut up. You're arrested. Take him to Ibiki."
"You old fool, you really think I'll allow you to take me in?" His words were met with a sharp blade slicing his neck off, nobody batting an eyelash as the head rolled around on the ground, the bandages unwrapping to reveal a Sharingan eye opened in surprise.
"He's lucky he's dead." The Hokage muttered darkly as he glared at the eye. "What the hell are you all standing around for? You three, get Naruto out of there and into the hospital. The rest of you seal down the facility. We'll open it later, when Naruto's recovered.
This is a new crossover I thought up, the only one of its kind I believe. Just don't ask me what happened to the rest of Rogue Trooper 'verse. Mainly because I have no idea, either.
Oh, and for those who think I'm a lazy bastard that puts things off as long as possible… you're absolutely right. I'll try to update something, but I'm not making any promises. If anything, expect another new story before updates of current ones.
Almost forgot, pairings open, NArutoverse only.