Approximately seventeen years earlier
The Third Great Ninja War had finally ended. After years of heavy losses on all sides, a treaty had finally been reached. Uchiha Obito, was supposed to have died years ago during the battle of Kannabi Bridge but was instead saved by someone who was also supposed to have died decades before. For months he was bedridden recovering from his injuries until that day. The day Nohara Rin, the girl he loved, was killed when she ran in front of his former teammate's attack. He knew she had done that on purpose to save the village but that didn't make it right.
Obito was consumed with grief. Uchiha Madara decided he needed to do something. If Obito was going to be of use for his plans he could not continue like this. After consulting with Zetsu, he came up with an idea. One that could help Obito out of his depression and be of use in the future. He sent Zetsu to obtain the materials needed.
Madara walked to the room where Obito had locked himself in since arriving back at the hideout covered in blood a few days prior. He knocked on the door.
"Go Away." He heard from the other side.
"Open the door." He said in a stern voice.
"No, leave me alone." Obito said in a hoarse voice from the other side.
Madara was out of patience. He kicked the door down and walked in to the room. "I said to leave me alone" Obito said not getting up from his bed.
"The girl, the one that died, how much did you love her?" He asked.
"Why do you care?" Obito said glaring at him.
"Answer the question brat."
After a moment of silence "She was everything to me. She was my best friend. She believed in me since the beginning. She looked after me when I got hurt and was there for me when I didn't have anyone. She never belittled me or mocked me even when everyone else did, and now she's gone." He said tearing up at the end.
"Did you want a future with her?" He asked trying to find the right moment to bring up his idea.
"Why does that matter?"
"Stop questioning me, I don't have a lot of patience." Madara said getting agitated at the young Uchiha.
"If she had given me the chance, yes. I would've wanted a future with her. Marriage, kids, growing old…" He said imagining what could have been.
"What if I told you, that's still a possibility?" Madara said.
"How?" Obito said his face brightening immediately.
"I sent Zetsu to go gather the required materials but I do need something from you. I need to run some tests on you to see if you are a possible donor." Madara said.
"Donor?" Said Obito confused
"I'm going to give your future, but in exchange I want you to swear your loyalty to me. I have plans to build the perfect world. One without wars. A world without suffering. A perfect Utopia. In order to build that I need your help and your loyalty and in exchange I'll give you the dream life you always wanted." He said.
"What do you need? I'll do whatever it takes."
"Whatever it takes?" He said holding back a smile.
"I'll do anything old man, Just tell me what I need to do." Said Obito getting out of bed for the first time in days.
"Follow me then" Said Madara walking out of the room.
Obito had no idea that at that very moment Zetsu was sneaking into the Hidden Leaf Village to obtain the materials Madara had requested. One was a scroll from one of Orochimaru's hidden Labs, and the other was a specific sample from the remains of one Nohara Rin.
The scroll was easy to obtain. Being able to phase through walls had its perks. Obtaining the sample from the grave was another matter. When Zetsu arrived at the cemetery, there was someone visiting the grave, late at night. It was the silver haired ninja from before, when he accompanied Obito to try and save his team mates.
"Rin, I'm sorry I haven't been by to see you. I've been assigned to Anbu and this is the first time in weeks I've had some time off. Minato Sensei is Hokage now and I'm serving directly under him. I think its his way of looking after me despite all the new responsibilities he has. I should leave, It's getting late and I still haven't visited Obito. I'll come back when I can." Kakashi said before looking up for a minute and walking away.
'If only he knew' Zetsu thought to himself.
As soon at it was safe, Zetsu performed a basic earth jutsu to unearth the grave. He unsealed the coffin and did as he was asked. He obtained the sample he needed and resealed the coffin. He placed it back in and reburied it making the grave seem exactly as it had before he had shown up.
Zetsu returned to the hideout and gave the items to Madara.
"There is only one thing missing, the surrogate." Madara said.
"Should I start the search?" Zetsu asked.
"The procedure will take some time. I already obtained the sample from Obito, and you have the sample from the girl, you just need to find a suitable carrier. Someone healthy and that won't be missed." He said.
"I'll start looking, shouldn't be too hard in this war ravaged country." Zetsu said disappearing into the ground.
A few weeks later
Zetsu was at a nearby town. There was a young girl, in her twenties, no family just passing through town. She stayed in towns for a few weeks and worked odd jobs to save enough money before moving on. She was perfect.
"Find the girl and bring her here. The procedure has to happen now."
"She is about to leave town, no one will notice her absence."
"The procedure shall take place tonight."
"And afterwards?" Zetsu asked.
"We let her go until its time. Then we retrieve what is ours and dispose of any evidence." Madara said sternly.
Hours later
Ellia woke up strapped to a table in a dark lab. She had been walking down the road to the next town on her way to the Hidden Leaf Village. She lost everything in the war and wanted a fresh start. A few miles away from her last town she had started to feel lightheaded and before she knew it everything went dark.
"You're awake." A voice said.
Ellia tried to get up, but failed to do so.
"Don't bother, you won't be awake for much longer." Said another voice.
"Who are you?" She asked terrified of what was in store for her.
"You don't need to know. What you do need to know is that you have been chosen for a greater purpose. The procedure you are going to go through is for a bigger purpose. And for that to happen," He said activating his Sharingan. "You need to stay in the next town for the next nine months or so until the birth. You will take care of yourself and most importantly; you will not remember any of this. If anyone asks about the father you say he was a ninja that died on a mission. Do you understand?"
"Yes." She answered obediently. Then genjutsu Madara used on her would keep her complacent and obedient. Now all he had to do was wait.
Nine Months Later
It was in the middle of the night when Zetsu appeared to Madara with the news that Ellia was in labor. Madara's health was deteriorating rapidly but he still had enough strength for one last task.
He and Zetsu left for the nearby town where Ellia was living. She was staying in a small home on the outskirts of the town for expectant mothers. When they arrived they heard screams of pain and the midwife telling her when to breathe and push.
'Won't be long now' Madara thought to himself.
Then they heard it, the cries of a newborn baby.
"It's a boy" They heard the midwife say.
"Uh wait a minute, he's not alone." She said a minute later.
Ten minutes later, there was another cry.
"It's a girl." She said handing the baby to Ellia.
"Little Kaien and Karan. They're so beautiful." Said Ellia holding her newborn children.
"Yes Thank you for taking such good care of them, but we'll be taking them now." Said Madara walking in with Zetsu.
"Who are you?" She said clutching her children close to her.
He activated his Sharingan and made her remember.
"You. Where am I? How is this possible?" She said looking at the babies.
"Like I said before, It's none of your concern." He said walking forward and taking the babies. "Kaien and Karan, They shall do nicely. Zetsu, dispose of the evidence."
As he walked away from the house, he could hear the screams and people begging for their lives before they were abruptly ended.
The children in his arms were sound asleep. 'They're a lot more quiet than their father' he thought to himself.
When he got back to the hideout he placed the twins in the room he had prepared a few weeks ago when he was only expecting one baby not two. They could share a crib for now, Obito could figure it out later. He would give them to their father when he woke up in a few hours. He had fallen asleep after hours of training. The twins would be his reward.
The next morning
Obito awoke to the sound of a baby's crying. He got out of bed and walked to find the source of the noise. He walked to a room he hadn't been inside before and found two babies in a crib, crying.
"I see you've met your son and daughter." Madara said walking into the room.
"My what?" Said Obito confused.
"Son and daughter, the future you wanted with Rin, those are your children."
"How?" Obito said.
"Don't look a gift horse in the mouth. They're here and your responsibility."
"How is this possible?" He said looking at the twins.
"You really want to know?"
"I obtained a sample from you and Rin and…"
"Rin's dead how did you obtain a sample from her?" Obito questioned.
"How do you think?" Madara said.
His eyes widened when he realized what he meant.
"You desecrated her grave." Obito said disgusted and stepping away from the twins.
"I gave you what you wanted, the how doesn't matter."
"I didn't want it like that, I can't do this." He said running out of the room only to be stopped by Zetsu.
"You can and you will. Those children can be of use to our plans. Even if you don't see them as your children they can still be trained and weather you like it or not you will do as you are told and take care of them."
"I won't." Obito said glaring at Madara.
Madara activated his Sharingan, "You will. You swore your loyalty and you will do as you are told, is that understood."
Obito clenched his jaw and nodded
"Good now look after Kaien and Karan, your children then go get ready for training." Madara said walking away.
"Don't call them that, I am not related to those abominations." Obito said picking up Kaien and realizing he needed a diaper change.