Lets see don't own Naruto and I don't own Spider-Man.
Peter Parker grunted, as he watched Norman Osborne as he tossed his weapon back and forth between his hands. The young teacher and part time photographer was currently on the top tier of the Brooklyn Bridge, off to one side he could see his best friend Johnny Storm trading potshots with Marko Flint. All four of the people were better known under their other guises though of Spider-Man, Green Goblin, Human Torch, and Sandman.
Green Goblin cackled from his demonic looking glider, as he tossed his pumpkin bomb toward the wall crawling vigilante. While the hero was dodging the explosive, the green and purple garbed figure was fiddling with a device. He watched as the hero flipped off of the side of the bridge and fired the device in front of the hero. He watched as a portal seemed to snap open and swallow Spider-Man up. His laughter was short lived though, as webbing shot out of the portal and blinded him. Without being able to see he lost control of the glider slammed into one of the cables on the bridge before falling the rest of way into the river. The device that had created the portal slipped from his hands and sank into the river. The villain snarled a bit, as he summoned the glider toward him. Once he was back on it he rocketed away. He had finally won.
"Spider-Man!" Johnny, the Human Torch exclaimed, as he rushed toward the portal only to watch helplessly as it snapped itself shut before he could manage to get there. The adventurer quickly slapped the communicator he wore on his chest into the on position. "Reed, I need you to get out here now with your gizmos and gadgets we have a portal problem."
Sand Man looked between the hero and escape, and decided that it would be better to leave the young man to his work of trying to find his friend than in trying to renew their fight. He quickly shifted back into sand, and simply fell into a passing truck and disappeared. The anxious Human Torch ignored the fleeing villain, as he focused on staying in this spot. Hoping that the portal would snap open again shooting Spider-Man out.
Hours later there were several heroes that had come by searching for the trail that the portal had taken, but were coming up empty in their search. Reed Richards, Dr. Strange, Iron Man, Forge, and Ant-Man had all come up with nothing from their various scans. Villains such as Dr. Doom and Baron Zemo who while they disliked Spider-Man, had a certain amount of respect for the hero and the idea that he would owe them for saving them had gotten them to try. They had the same amount of success though, as everyone else seemed to have. Wherever Spider-Man had disappeared to, he had left little if any trail for anyone else to follow.
"Without Osborne and his teleportation device, there is nothing more we can do." Doom declared, as he looked at the assembled figures that had gathered to figure out what they should try next. "It would be best if you were to accept the loss of your ally and continue on with your lives. The one known as Spider-Man is either dead or lost within the fold of reality." He explained to the heroes.
"Spidey wouldn't do that to us, no way I'm doing that for him." A flaring Human Torch returned to the armored figure in anger. Ice Man, Wolverine, Daredevil, and Firestar all nodded their heads in agreement with the youngest member of the FF.
"We're going to do our best to find and rescue Spider-Man Doom." Captain America returned to the armored dictator. "Now you can either help us or you can get out of the way."
"Bah," Doom returned to the hero, "the annoying arachnid is gone, and you are merely going to have to accept that little detail of life."
"Really Victor, and how many times were you killed or lost in alternative places?" Reed Richards questioned his nemesis.
"The difference is that Spider-Man has nowhere near my intellect or strength of will though." Doom returned to his hated rival. "If you wish to continue with this fruitless and pointless search for one who is gone though, be my guest. Without the device though, the task is near impossible, even were one such as myself. There are simply to any places that a portal could have sent him. We don't know if we should be searching alternate realities, or if we should be searching other spectrums or phases of this reality, or even wait for a phone call or find that he has been lost in time. Without knowing these things, there is little that can be done to figure out where he has gone." The dictator then stormed out with his cape billowing behind him.
Baron Zemo nodded his head in agreement. "Zhe man be correct, zhere's nozing more to do than to tell his family."
Johnny looked like he was ready to lunge at the armored figure, but was being held back by his friend. "Not now kid." The rocky figure of Ben Grimm told his teammate. "You ain't going to get anything from beating on him now, no matter how enjoyable it would be."
The elemental being nodded his head in agreement before turning away from the man. "Reed?" He questioned hopefully.
"We're not done looking Johnny, but it will take a lot longer than we originally thought." Reed Richards explained. "The reason we're having so much trouble with it though is because that it was an extremely unstable portal to begin with. Even once we get the right frequency, there's no telling what kind of effects that it might have had on Spider-Man. Doom was right in the fact of not knowing where the portal was supposed to send him makes it even harder though."
Johnny nodded his head in acceptance of what the man was saying before he stalked off. The others could only shake their heads at the hero as they focused on trying to find the missing jokester.
In another dimension: Village of the Leaf Hokage's office.
The Third Hokage was in the middle of doing something that every person that gained the office hated. The dreaded daily paperwork that they all were forced to deal with. A strange glowing circle appeared over his desk. The old man moved with a swiftness that few would have believed that he was still capable of as his Anbu guards dropped from their hiding places and landed between the swirling mass and their leader.
"What is it?" One of the ninja questioned curiously as no attack seemed to come out of it.
"I do not know," the ninja known as the Professor admitted to his guards as he examined it. It looked similar to a chakra barrier, but lacked the feel of any chakra then there was the fact that it was only on one side near his desk. If it had been an attempt to capture him, then it was clearly a deficient attack. As quickly as it had formed the swirling thing spat something out, and then disappeared. The third watched in disbelief as the thing barreled though several piles of paperwork creating a storm of paper in the office. The ANBU cautiously stepped forward, and saw that the thing that had landed in front of them was a young child.
The boy appeared to be no older than 7 or 8 and was dressed in an oversized red and blue uniform that was similar to some of the clothes that shinobi wore with insect like symbols on the front and back of them, and an interesting web like design as well. He also wore a mask that like the rest of his clothes were much too big for him, the mask had odd places for the eyes that were made out of an unknown reflective white substance that he couldn't identify.
"What shall we do with him Lord Hokage?" One of the ANBU questioned the man curiously.
"Take him to Interrogation, but tell them to treat the boy gently and that I want someone to oversee his questioning." The old man told them with a warning in his voice that the ninja nodded their understanding to as they disappeared in a blur of speed as they took the boy to be questioned. While the questioning happened the Hokage had various sensory type ninjas search for how the unknown boy had managed to slip into his office nearly undetected.
It was several hours later when a ninja finally returned with a report for the old man. "Well?" He questioned, as he lit his pipe up and looked the ninja over questioning.
"The boy has no memory sir," the ninja returned, "he has a few flashes, and knows things that no one I know of has heard of, but the memories that go along with the knowledge is gone." The ninja explained to the third. "He has highly developed chakra coils, and basic training or knowledge of most of the basics that ninja his age should have. When the Yamanaka interrogator went into his mind there was next to no memories, but he's a trove of knowledge once you can get past his defenses that is."
"Defenses," the third questioned with interest. "I thought that there were no known defenses against the Yamanaka mind jutsus?"
"So it was thought Lord Hokage," the ninja agreed, "however, this boy though has managed to do just that."
"I see, and what has the boy told you about himself?"
The ninja shook his head at this. "The boy is very confused at that, and has given us the strange name of Parker as his family name, and Peter as his personal name."
"I see, and what of his attire?" The Hokage asked with interest.
"Nothing is known about any of the objects that he had on him sir, nor could we determine where they were manufactured. We have inspected everything on the clothes and compared them to everything in our records. The crest upon his chest and back are like none that are in any of the village archives, we also asked the Aburame clan for any help in identifying the symbol, but other than saying that it is similar to a spider and that there are no known spider using clans they have had nothing to offer. The boy also appears to have an unknown kekkei genkai."
"Is that so?" The old man questioned with interest, it was rare for a boy to have an active bloodline at his age.
"Yes sir, the boy already has strength levels that are several time stronger than an average adult shinobi, his gymnastic skill already exceeds a trained gennin, he can stick to walls without using chakra, and he has some sort of ability to sense attacks, it is similar to the Byakugan except he cannot see the attack only reacts to attacks. As I said earlier he has assorted levels of knowledge, his reading and writing skills though are odd he was taught in an unknown language and will need to be taught to read from scrolls."
"I see, very well put him in the academy for now, if his chakra reserves are as high as you say, he could prove to be quiet a valuable asset to us." The old man suggested knowingly. "Have someone keep an eye on him and set him up in one of the abandoned apartments. Who knows, this could be just the sort of thing that Naruto needs." The man spoke optimistically, as he chewed on the end of his pipe. "Place him in the same building as Naruto, unless he objects for some reason. Be sure to have someone keep an eye out for him though I would rather be cautious with this new boy than to allow him to be to free in his access. If he proves to be safe then have someone sit and teach him to learn how to read and write."
"As you command Lord Hokage." The ANBU replied with a bow, before he disappeared.
The Third sighed and wondered how long it would be before a member of the Council decided to come in and demand to know about the boy. From what he had read, and what his gut told him, he thought that this boy had great potential if he was merely given the chance to use it. After all of the ninja they had lost over the years, particularly in the last war, and in the battle against the Kyubbi, they needed every ninja that they could to replace those that were lost. He knew that there was a chance that members of the Council would try and take control of the boy later on with his potential, particularly with his most unique bloodline. The Abrume Clan would likely be amongst the first to try and claim the boy unless they decided that as a spider type he was some sort of natural enemy to their bugs. There were others including Danzo that would try and take the boy. He had to be ready for them though. The addition of having a secret or unknown language would appease both Ibiku and Danzo though.