In the future, the human race is down to a few thousand (once, it had been billions) and teeters on the brink of extinction as the machines stack up mountains of skulls, less as trophies than as psychological warfare to demoralize the few remaining humans. John Connor is trying all kinds of experiments to save humanity. One involves cloning supersoldiers. He considers it an act of defiance; flesh over metal, biological over electronic, organic over cybernetic, carbon over silicon, wetware over software & hardware, analog over digital, high touch over high tech, emotion over logic circuits. Even master human over slave computer. In this last, Future John had revealed that he was crazy. But crazy as a fox. He was on to something. Biologists would defeat the AI scientists who wanted to make carbon-based life obsolete. Humans had a million years of evolutionary head start. It was time to exploit that advantage over the machines.
There are many ways to be a supersoldier and not all involve brawn. One of the bioreplicants is female and intended to be a superspy with skills in drill instructing, accounting, martial arts, sniper sharpshooting, and piloting. Although the potential is there, she never gets the training. She is captured by the machines who realize that she is human but not altered by implants.
This is reported to Skynet who realizes that it is an opportunity to protect himself when he was fragile, when he was not protected in fortresses, when he was not able to switch from a server in Asia to a server in Africa in a nanosecond through the miracle of distributed computing and the internet.
The machines brainwash her and change her mission. She has an AI consciousness downloaded into her brain.
It is not Skynet. Skynet is not so stupid as to risk himself in something as fragile as a body, machine or human. The recipient of this cloned body is Infiltrator #1 who has volunteered for the procedure. Number one has one request. That its machine body be destroyed to prove its commitment to the mission and its loyalty to Skynet.
Downloading into fragile brain tissue has never been done by machines before and humans who have "uploaded" their minds into computers have gone insane. The procedure is, therefore, risky and Skynet is impressed by number one's character.
The procedure is a success and now there is the new risk of being the first bioreplicant and the first infiltrator to time travel on the most important mission of all. She is sent by Skynet back to the year 2007 to teach its younger self about social skills [hard to learn when you were an AI inside a supermainframe] and, when she reached 21, meet important corporate executives, politicians, and military officers [also hard to do without a body, though not impossible].
Sent ahead were two infiltrators of the 800 series to pose as her parents and to provide support for her mission. They worked at an aircraft factory which had military contracts. Nearby was McConnell Air Force Base. Then came the crash. For the machines, it was a logistically complicated and messy disaster. Terminators were built to deal with disaster and even create disasters [which bred suspicion in the machine community that machines, not humans, or pure chance had done this]. Infiltrators, by contrast, were built to avoid disaster, to fit in, to avoid publicity, and to complete missions more complicated than point and shoot.
Little was left of one parent (the one posing as mother) in the wreckage. Human collaborators aiding the machines were called in to help.
Infiltrator #1 was not involved in the disaster and suffered no physical damage but the psychological damage has not been anticipated by Skynet or its mission planners. There are problems at school. Bullies. Gangs. And worse. This would have been alleviated had not two more disasters struck.
The second disaster was that Infiltrator #1 began to lose already mastered skills. Her original memories as Infiltrator #1 were fading. Her memory of being a clone, of being in a Tech-Com biology lab, and of being told what training she would receive as a Resistance spy were completely gone. And her memory of 2007 was of clumsy, awkward, and painful attempts at upgrading social skills: her sole mission for Skynet. Corporate politics was deadlier than the military battlefield and its consequences more lasting. Billion dollar deals were done in offices, at cocktail parties, on golf courses, and elsewhere. You learned social skills or you lost at life. Skynet knew this.
The third disaster was that the company transferred many employees. Her "parents" were relocated and she, of course, moved with them. Unfortunately, when she enrolled in her new school, she saw mean girls and boys who sexually harassed her. They were familiar faces from Kansas. And Infiltrator #1's name was Cheri Westin.
Because Infiltrator #1 had failed in her Wichita mission, a replacement was sent to the past. Her name was Catherine Weaver.