When the boy was 8 years old, he was in a fire that consumed most of the downtown Shinto of Fuyuki City. It was a terrible accident in which most of the residents were killed and even those who were rescued died soon afterwards from their injuries. There were no survivors except for a boy, and a girl who was found under him as he tried to shield her body from the flames. The lives of these two children were amazingly spared, however the girl was in a coma and never regained consciousness. As for the boy, he was completely paralyzed by the burns at had crippled his body.
When the boy's injuries had healed, he suddenly became aware of the situation and the effects the fire had on his life. His family was in all likelihood dead and even if they weren't the trauma from the flames had erased his memories, leaving him without a way to identify them or his next of kin. It was difficult for the lad to accept all this in his young mind but he tried as best as he could.
It was then that he began to think of the little girl who was sleeping in the bed next to his, this child who was in the same straits as he was, as his only friend in the world. "Please, let her wake up." He prayed that again and again as he was forced to watch her sleep without being able to help her. A while later, the poor girl's condition took a sudden turn for the worse and she was taken to the emergency room.
The next day a doctor came to him and offered him a choice, there was an experimental procedure that will allow them to completely replace his paralyzed body with a synthetic one. Despite to regain some control over his life, he agrees and they begin the operation.
That day a boy known only as Shirou and a girl by the name of Motoko Kusanagi became the first two human cyborgs. Shortly after their operations, they were paired up to provide mental and emotional support as they made their way through the two year physical rehabilitation process. It was the start of a friendship that would last a lifetime, and to the knowledge of a select few, it turned out to be so much more then simply that.
Later on...
Lemon route: Shirou and Motoko become the first recorded instance of a sexual encounter between two cyborgs, it was reported to be "clumsy, awkward, slightly painful at first and totally worth it afterward" by Motoko. They are also the first to realize that having cyber sex with the opposite sex is dangerous, due to the nerve incompatibility between sexes from having some unique organs present in only that sex. It was really, really hot.
Crack route: Starts and proceeds the same as the lemon until Motoko straddles Shirou and proceeds to relieve him of his clothing. Foreplay happens until Motoko realizes a small oversight on her part, their cyber-bodies are not built with perfect human biological accuracy in mind. As both of their bodies are technically lacking the "equipment" needed to have sex she decided to correct this oversight. It ends with her holding a division of scientists at gunpoint while screaming demanding that they create bodies that would allow her to indulge in her more carnal impulses. Shirou gets dragged along so they can get started as soon as the bodies are finished. Fear a sexually frustrated Motoko, fear her.
possible line:
"Make it BIG. Long and thick enough to split me in fucking two! I swear if I'm not satisfied when this is done, I will personally come back here and shove it up your asses until you GET. IT. RIGHT. Do you understand me?" Motoko ranted.
The scientist nodded fearfully in the corner, crying at the abuse from the cyborg teenager as Shirou tried to apologize.
"Now you!" she said pointing at Shirou, "Keep me occupied until they finish, this may take a while."
Shirou knew better then to argue right now...