The Prototype is a 9 fan work written by Franki Lew in 2010. The story is a prequel to the film "9" by Shane Acker, which follows the events of a much younger 1 and 2 and their interaction with a female stitchpunk.
The story is separated into eleven sections all named after a certain theme in the story.
1 and 2 (at the time younger and more stable stitchpunks) are separated from their creator. While trying to survive the ongoing war between man and machines, 1 is shot in the knee. 2 drags his crippled friend through the war grounds until they come to an abandoned mansion. While tending to 1’s wounds 2 hears a ringing sound coming from the darkness. Following the sound 2 finds a visually impaired, female stitchpunk who wears a Christmas bell around her neck. Thrilled to meet others of her kind the female stitchpunk allows 2 to stay in her home and helps tend 1’s knee. 2 decides to name the stitchpunk “Pro.” for the letters on her chest.
2 and Pro. become fast friends, Pro. showing off a flower bud she’s been tending to since she came to the mansion. 2 realizes that Pro. is mentally traumatized by something she prefers not to talk about.
Meanwhile, despite her affection for him, 1 is disgusted by Pro. and doesn’t want to make friends with her. It isn’t until he finds out she helped him while he was unconscious that he starts opening up to her. 1 and Pro. start forming a fast friendship as 1 also realizes the importance 2 has on his life.
Eventually the walker machines demolish the mansion and 1 and 2 have to convince Pro. to leave. 2 finds out that it was her experience in war and destroyed optics that caused Pro. to lock herself away in fear of the outside world. 1 and 2 eventually do convince Pro. and the trio heads out in hopes of finding their creator. Before they get very far however, Pro. is shot by a walker and dies as 2 tries to fix her. 1 and 2 give Pro. a funeral and incinerate her body but spare her Christmas Bell. 1 disowns 2 and they continue their travels without Pro’s company.
Seven to eight years later, 9, 7, 3 and 4 find take shelter in Pro’s mansion. While exploring the inhabitants of the mansion 9 comes across Pro’s flower bud that blossomed into a beautiful flower.