Madara should have known that Orochimaru would have found where the former leaders of the Uchiha Clan were buried. Considering the nature of the Sannin's experiments, it was only a matter of time before he turned his eyes away from the remains of the Senju and towards those of Konoha's other founding clan. Fortunately, he had gotten wind of this experiment before the other man's plans in that regard could go too far. Sarutobi Sasuke's son would eventually get wind of what his former student was doing, but based on the man's past behavior, it probably wouldn't happen until it was far too late for the one individual that concerned him. Sarutobi Hiruzen was far too soft-hearted, and nothing like his father who had been a worthy adversary at all.
As Tobi who would be his representative from this day forth, his living avatar who would be the one to deal with the day to day forwarding of his plans until he was revived at the right moment fought the Yondaime and did his best to raze the village with the Kyuubi which was a task he longed to do but was too old for, he snuck into one of Orochimaru's secret facilities. After ghosting through the empty and mostly silent halls, he came to the room that contained what he searched for this night, that which Orochimaru had regarded as more of an intellectual exercise than anything and hadn't yet found a use for, clones of the heads of the Uchiha clan, clones that at the moment were mere infants.
After double checking that he'd got the right batch of infants, he went down the short row of babies looking for a certain one, one whom he'd been handed and told would be his responsibility to protect and help grow when he was nearly four. Being of the same line, they were all similar, with his father's clone being the most alike, but he knew Izuna's Chakra like he knew his own, and even with the miniscule amount that these little abominations who would grow up never knowing what they were possessed, his brother's copy who had been made from a piece of his brother that had been stolen from his grave shone out to him like a small beacon.
When he'd learned of the experiment, he had contemplated killing the boy, but his brother was one of the few things he cared for, and the thought of having a living piece of his brother in the world that he'd been gone from for so long had been comforting in a way. Right up until he had looked down in the bassinet that had undoubtedly been stolen from the hospital, the decision to let the clone live hadn't been set in stone. But, when he saw those wide dark eyes staring up at him, he had found to his surprise that he was gently lifting the infant from the bassinet and cradling it in his arms as he had done with the first Izuna back when he was a baby rather than lowering a kunai towards it for a fatal strike.
He hadn't known what to expect when he first held his brother's clone in his arms. Considering what he'd read about cloning, he'd known not to expect much, but when the eyes that had belonged to his brother held no recognition, and the infant began to fuss over the fact that it was being held by a stranger rather than calming down and falling asleep like his little brother used to, it had hurt. He didn't like the pain that he felt over the fact that the one person in the universe that should always be able to recognize him didn't, so he decided to do something about it. That something involved theoretical exercises involving improvements and out branches of a certain jutsu of Senju Tobirama's, and the clone of his grandfather. He'd never liked the man all that much the first time around, and his clone would be far more useful in death than the man had ever been in life.
When the deed was done, he departed from the woods where he'd done it after leaving Orochimaru's lab with a pair of pilfered infants and found and hired a wet nurse to deal with the things his brother could not take care of on his own due to the fact that he was inhabiting the body of an infant.
After dealing with a number of important tasks in preperation for his passing, he returned to the home of the wet nurse who had lived in an out of the way village in a remote corner of Fire Country three years later, reasonably confident that his brother would now have control over his biological functions, would be able to feed and dress himself, and would be ready to travel with him. What he found when he arrived at the wet nurse's home however was what seemed to be a normal three year-old child who talked a mile a minute in toddler babble, couldn't tie his own shoes, and who apparently didn't recognize him if the question of "Who are you?" which he didn't answer was anything to judge by. The only reason he could think for why this had happened besides his complete failure to house Izuna's soul in its body where it belonged with the experimental seal and jutsu combination that he'd created was that an infant's mind wasn't equipped to handle the memories of an adult and so had gotten rid of them.
After accepting a piece of macaroni art from the small boy, he slunk away disappointed, but with vague notions of taking the child on as his apprentice when he returned, as the boy was his brother's blood. To that end, he had ordered the wet nurse to send the child to Suna for ninja training when the time came as he departed never to return.
As he left, he never saw the expression on the child's face as the small boy found himself wondering why he was thinking of the older boy who had pushed him over while he was walking, and had picked him up and held him while he cried over his hurt knee, and associating that boy with the man who was walking away. If he had paused in that moment, he would have known that the memories were there, but mostly blocked by the small mind that couldn't yet understand most of them and therefore pushed them away until it could get a grip on them, rather than risk breaking, and that almost every time the small boy experienced something familiar in his life, a similar memory from his old life would return, filling in yet another piece of the puzzle and bringing another small part of his brother back.
As Madara disappeared beyond the Horizon, an inexplicable sadness overcame a small boy named Izuna, and for the first time since he'd gotten past his terrible twos, he didn't smile happily as he was given a new toy or his favorite food at dinner or allowed to play with his toy boats during bathtime.
As things turned out, Izuna was not dragged to Sunagakure to be trained as a ninja when he was six as the wet nurse had been ordered. This had been because less than a week after Madara had visited and left for the last time before his planned resurrection, the woman had died in a household accident while he was out playing on the lawn. The woman's neighbor - believing that the child would have better chances in Konoha - gave Izuna to a border patrol unit as they were passing through on their way back to the hidden village.
While she was bathing him shortly after they arrived back in Konoha, the squad leader who'd been considering keeping him noticed a seal on the boy and brought him to an expert she knew since she couldn't make heads or tails of it. The expert then brought the boy to another expert who brought him to the Hokage. After a thorough examination, the Hokage decided that there was nothing to be done about it at this time.
Since the seal didn't seem to be hurting anybody - as the boy seemed to be an ordinary three year-old albeit with some odd memories - the Hokage deemed it safe enough to leave the boy at the orphanage.
Had the villagers been a bit kinder and a little less distrustful of things that were slightly out of the ordinary, Izuna's arrival at the orphanage probably would have been the end of it. He'd been given a good second chance at life, and by the time he would have had all of his memories back, he would have been happily making his way through a civilian school. Every afternoon after school, he would have been helping out an old man who would have trained him in a job that he loved and hadn't had the opportunity to do the first time around because of the life he'd been born into in return. Had his hypothetical life continued in this somewhat idyllic manner, Tobi wouldn't have bothered him since he hadn't been told about him because he wasn't necessary for the plan, and by the time Madara was resurrected, he wouldn't have had the time to take him as an apprentice as he would be brought back in the midst of battle.
Unfortunately for any plans for just such a civilian life that Izuna may have had in the future, rumors about the purpose of the seal that the ninja who had brought him to Konoha had discovered had spread. By the time Izuna had reached the orphanage, the story of how he'd been used to resurrect the spirit of a dead man and how that man's soul was now trapped in his body replacing the one he'd been born with had gone from one end of the village to the other. Speculation on who this person who had been resurrected through this horrific technique was and how evil he must have been to condone such a thing ran rampant. When the matron of the orphanage had looked at the boy who had been delivered to her and noticed that he had eyes that were "far too old" for a child his age, she had decided to separate him from the other children and put him in with Naruto as there were no other free rooms available, and the blond brat who had tried to set his mattress on fire the week before could look after itself. As far as she had been concerned, she wasn't about to allow a man whose identity was as yet unknown sleep in the same room as and potentially harm the children under her care on her watch.
As Naruto tried to understand why the orphanage staff had put another bed in his room, Izuna stood in the doorway of what was to be his new room and stared at the other boy who was to be his roommate. He'd never seen hair that shade of yellow before.