The Leyte project was initially designed by a multinational company lab based in Salem working to build a effective cloned soldier program, using samples from an anonymous source with several shady groups backing them. The main goal was to create many clones with superior genetic make-up yet being able to easily be made and adopting artificial memories and a training program with as much speed and effectiveness as possible. Unfortunately, second impact interrupted the production stage after a first generation had been finalized. It spent three years on the new sea floor before successfully recovered by one of the companies largest backers, NERV.
With their advanced technology, science teams and lack of scruples, they quickly picked up on where the project was left off, and improving on it greatly, twisting it for their own upcoming purposes. Additions to the genetic information, tweaking it so that the ageing would slow down enough to be usable in a few years that would allow for additional training and mental development instead of being rushed out were simple due to how well the project had been sorted for ease of duplication. Hard work was done to make sure it would bond with an Evangelion well, and as much as possible, it was tweaked so that it would be inclined towards being gullible for ease of ensuring loyalty.
Log of New Leyte project, day 3
[Redacted]: "The fetuses have already started developing features. However, there are some problems with them."
[Redacted]: "Such as?"
[Redacted]: "They lacks a lot of non-essential cells. The disposable nature meant they didn't expect them to have time to heal naturally and lacks a lot of white blood cells"
[Redacted]: "That's going to make them a lot weaker."
[Redacted]: "Actually, it won't. they're designed with this in mind. It could probably run and jump better then a lot of security we have now. It just won't heal quickly."
[Redacted]: "We'll just have to make a lot of them."
[Redacted]: "They're not actually that replaceable. There are other problems, though, signs of ALDH2 polymorphism-"
[Redacted]: "What's that?"
[Redacted]: "Basically, it can't handle alcohol."
[Redacted]: "…Do you plan to get the under-aged child pilot of a forty metre tall invulnerable robot drunk before missions?"
[Redacted]: "No Sir, no, but, there's more-"
[Redacted]: "Get back to work and do not bother me again until you have something important to report."
After another year of hard work, it finally started producing cloned bodies, the majority being kept in storage while several were raised from the state of newborns to about two years of development within a year in slowly thinning numbers based on early performance tests. By the current Leyte's second year, he was one of the last of the clones deemed finest and most suited for starting the real work. Conditioning.
The remaining clones were spread out so they would remain unaware of their nature, in hopes that this would encourage some self preservation. Training consisted of a lot of abusive treatment, instilling the idea of devoting themselves to tasks with frightening focus, which went well, though glitches did occur with some tasks, such as one almost starving to death when given a videogame to 'pass time'. When discovered, they attempted to correct these whenever possible.
Log of New Leyte project, day 2,341
[Redacted]: "How is he doing?"
[Redacted]: "Really well. He's developing nicely given the ageing and actually likes training."
[Redacted]: "Cool. Oh! Here, I got coffee for the late shift today."
[Redacted]: "Ah thank you, you're an angel"
Records then show a spike of adrenaline within Johann-03, as well as blood loss from several lacerations, followed by minor bruising to the waist.
Cameras show subject burst through the observation window, tackling [Redacted] and attempting the stab her in the chest with a pen before [Redacted] stopped him with a sudden tackle. [Redacted] was uninjured.
When it was time for public schooling, the clones had mostly been put in storage to be given memories from the primary sample, Johann-01. Johann had a successful record and did especially well at sports, showing he clearly had developed at least some of the abilities suited to a soldier he had originally been made for, social development was never very notable, but psychologist reports suggest this is more of a product of being raised by scientists and soldiers, rather then something more sinister.
It was not long after this point that his Eva was theoretically completed and ready for basic testing, travelling to Germany where it had been constructed, an Angel attacked the NERV base there. He, and a second and equally unprepared pilot were dispatched in their still unfinished Evangelions. The fight was very short and messy, both evangelions and pilots sustaining major damage, resulting in the loss of Johann-01, whose remains could not be found after a spike in his sync ratio, followed by several explosions leaving the Eva severely damaged.
Many months later, Unit 06, now modified with enhanced durability and a synchronization inhibitors, to accommodate problems discovered in the first test, was delivered to NERV Boston, where Johann-02, Unaware of its previous pilot or his theoretical trip to Germany awaited his first chance to test the unit.