In an alternate 1930s world, a scientist is ordered by his dictator to create a robot in the apparent name of progress, and so the scientist creates the B.R.A.I.N., a highly intelligent robot. The dictator seizes it upon its apparent completion, and turns it into the Fabrication Machine, an armature that can construct an army of war machines to destroy the dictator’s enemies. But the B.R.A.I.N. is seized before the scientist could give it a soul, thus causing the Fabrication Machine to decide to exterminate all of Earth’s population. The Fabrication Machine reprograms the other war machines to attack humanity, wiping out all plant, animal and microbial life with toxic gas and chemical weapons. On the verge of destruction, the scientist uses alchemy to create nine homunculus-like rag dolls known as “Stitchpunks,” giving them portions of his own soul via a talisman he created. He dies upon completion of the final doll.9 2009.
Some time later, the final Stitchpunk, 9, awakens in the workshop. Taking the talisman with him, 9 ventures into the devastated city and meets 2, a frail inventor who gives him a working voice box and is surprised to see the talisman. The last active machine, the Cat-Beast, attacks the pair and abducts both 2 and the talisman. 9 collapses, but awakens in Sanctuary, the tower of an empty cathedral that is home to other Stitchpunks – the dogmatic leader 1, his large bodyguard 8, the cycloptic engineer 5, and the mentally unstable oracle 6. 1 immediately declares 2 as dead, but 9, having seen the condemned factory where the Cat-Beast took him, decides to rescue him. 9 and 5 venture to the factory where they find 2. The Cat-Beast attacks the trio, but are saved by 7, the only female of the Stitchpunks. 9, drawn by curiosity, connects the talisman to the derelict Fabrication Machine, reviving it, and it subsequently kills 2 by sucking out his soul. 9, 5, and 7 manage to escape the factory.
7 takes 9 and 5 to an abandoned library, where the silent scholar twins, 3 and 4, have taken residence, and show 9 the Fabrication Machine’s origins.