Warnings for chapter: character death, violence.
15 years later...
The farm at the end of the dirt road was small, sitting near the crest of a gently rolling hill. A tiny single-level house and small barn capped the hill overlooking the field. There was one farmer working the field, a man in shabby coveralls and a beat up hat, with long, dark hair tied in a messy ponytail. Barely visible in the window of the house was the silhouette of a woman.
The farmer paused in his work, wiping the sweat from his face with a rag. His dark eyes drifted across the field and suddenly stopped, fixed on the figure in a black, hooded cloak standing on the other side of the fence.
"Can I help you, stranger?" he asked, approaching the fence. "You lost?"
The cloaked figure shook its head and held up a pair of photographs in his right hand. "Have you seen these two?"
The voice was young, male – probably a teenager, no older than the dark-haired boy and redheaded girl in the photographs.
"Not sure I can help you there, kid," the farmer said with a sniff as he looked away. "We don't see many folks out here. You might have better luck in town."
The cloaked figure silently looked at photos in his hand and then shoved his whole arm forward, photos extended. "Maybe it would help if you took a closer look?"
B3-116 glared up from the cloaked figure's exposed wrist.
The farmer hesitated a moment and then reached out to take the photos with his right hand, the faded numbers B2-012 visible. He looked at the photographs for a few moments and then raised his eyes to stare into the depths of the hood. "Tell me," he began, "What will you do when you run out of us to kill? Will they make you turn your blade on yourself?"
The cloaked figure didn't answer. Then, in a single, lightning-fast smooth movement, he drew a sword and cut the farmer down. He watched the body fall, crumpling to the ground in a spreading halo of red blood.
A second cloaked figure dropped down to the road from the trees, red hair trailing from under her hood. "What did he say to you?"
"Nothing," the cloaked figure said after a moment's pause, turning his head to look at her. "Where is the other one?"
She made a hand seal and then pointed towards the house. "There. Heading out the back of the house, towards the forest."
He nodded, flicking the blood off his blade, and started towards the house.
And that brings us to the end of Replica. I hope you enjoyed the ride.
I suspect you will have questions, especially considering the ending and the epilogue.
Who's the real villian?
Umbrella Corp - just kidding.
No really, there is no one real villian. Pay very close attention. While Danzo, Orochimaru and Madara are implied to be involved - Madara knows way too much about the identifying tattoos and the facility's history for his hands to be clean, not to mention he's a master manipulator - the facility itself is hinted as early as its first appearance that it's of civilian origin. Naruto and Sakura both note some of the equipment would not be found outside the civilian sector. And even if these three villians were eliminated, there is a possibility the private civilians doing the research will still exist, as hinted by the appearance of Sasuke "B3-116" in the Epilogue.
What is the purpose of the copies?
It's implied in a few places. The copies of a younger Sasuke, Batch 1, were made for their eyes. Batch 2, as implied by Ino and suggested by Kakashi, were meant to be used as weapons. Specifically, as a hunter/tracker team. They were stripped of memories in order to facilitate easier reprogramming. Batch 3's B3-116 duo are an example of what they were meant to be used as.
You can also tell how the facility was trying out the seals on them.
B2-001, who are killed by Madara, only have the dead man's switch and the vigilance seal.
B2-002, found by Suigetsu, have the dead man's switch, vigilance seal, and the memory seals.
B3-003 and on have pretty much the works.
Are the Sasuke and Karin that get away at the end of chapter 8 the originals? If not, where are the originals?
That is up to you to decide.
Although, to be fair, the copies are matter replicas - they all are the originals, at least to begin with. It's only after the serial number and seals are applied that they stop being "Sasuke and Karin."
Will there be a sequel? If so, will we find out the truth there?
No, not as of yet. If I do one, Sasuke B3-116 will likely be the focus.
The following is the official timeline of the story:
-3 days: Juugo and Suigetsu are separated from an injured Sasuke and Karin
-2 days: Madara finds the copy set designated B2-001; an unknown male sells a merchant the copy set designated B2-002
-1 days: Suigetsu and Juugo split up to search for Sasuke and Karin.
0 days: Juugo infiltrates the forest facility and is wounded retrieving copy set B2-003; they are sent to Konoha by the Sasuke Retrieval Squad. Suigetsu rescues copy set B2-002. Sasuke Retrieval Squad enters the facility and liberates copy sets B2-004 through B2-054 and the suspected original Sasuke and Karin. Madara kills copy set B2-001. Tsunade wakes up; Suigetsu and set B2-002 meet up with the escapees from the facility. The Facility is destroyed by Konoha ANBU; Madara retrieves the suspected originals and disappears.
Plot of Naruto resumes as normal.