In a unique alternate reality set in the 1930s, a nameless scientist, portrayed by Alan Oppenheimer, is forced by a ruthless dictator, Tom Kane, to create a highly intelligent robot in the name of progress. Following the dictator’s orders, the scientist develops the B.R.A.I.N., a machine built from his own intellect, granting it the ability to reproduce other machines. However, upon completion, the dictator seizes the creation before it can be endowed with human traits, such as a soul, transforming it into the Fabrication Machine, which constructs an army of war machines aimed at obliterating any opposition.
Lacking empathy and a soul, the Fabrication Machine chooses to eliminate Earth's entire population, unleashing waves of toxic gas and chemical attacks that devastate all plant, animal, and microbial life. As the looming threat endangers the planet, the scientist utilizes alchemy to forge nine Homunculus-like rag dolls, referred to as Stitchpunks, infusing them with fragments of his own soul through a special talisman. Tragically, he dies as he completes the final doll.
Eventually, the last Stitchpunk, known simply as 9 and voiced by Elijah Wood, awakens in the scientist's devastated workshop, surrounded by the ruins of a once-thriving city. Grasping the talisman, 9 bravely steps into the outside world, where he encounters 2 (voiced by Martin Landau), a malleable inventor who successfully provides 9 with a functional voice box. Their initial reunion takes a dark turn as they are the target of the fearsome Cat-Beast, which abducts 2 along with the talisman. In a moment of desperation, 9 collapses but then wakes again within Sanctuary, a tower standing within a crumbling cathedral, where he meets other Stitchpunks: 1 (the zealous leader, voiced by Christopher Plummer), his formidable bodyguard 8 (Fred Tatasciore), the engineer with one eye 5 (John C. Reilly), and the disturbed oracle 6 (voiced by Crispin Glover).
1 quickly declares 2 to be dead, but 9, fueled by determination and having discovered the factory where 2 was taken, resolves to rescue him. Teaming up with 5, 9 returns to the factory, where they are met with another Cat-Beast. Just when it appears they would be overwhelmed, 7 (an intuitive warrior portrayed by Jennifer Connelly) steps in and vanquishes the creature. As curiosity drives 9 further, he activates the talisman on the dormant Fabrication Machine, unwittingly reviving it, which tragically results in the loss of 2's soul. Together with 5 and 7, 9 narrowly escapes and they retreat to the abandoned library, where mute scholar twins 3 and 4 reveal vital information about the origins of the talisman through a film showcasing the Fabrication Machine’s dark beginnings.
The group grapples with the consequences of their actions as the Fabrication Machine begins sending hordes of mechanized enemies, leading to an intense battle against the bird-like Winged Beast, which they ultimately overcome, but at the cost of their sanctuary. As they regroup in the library, 6, along with 3 and 4, reveals more cryptic details about the talisman's significance. Meanwhile, the Fabrication Machine repurposes 2's lifeless body into a hypnotic trap through another machine, named the Seamstress, leading to further tragedy.
Just when hope seems lost and more Stitchpunks are captured, 9 revives a fighting spirit, going into battle solo to take down the Seamstress and rescue 7. However, the horrors continue as the Fabrication Machine persists in its destructive path. In a climactic moment, the surviving Stitchpunks work together to eliminate the factory. Despite their victory, they soon face the revived Fabrication Machine that absorbs 5's soul. Through a series of heart-wrenching events, they lose more allies, yet 9 persists, guided by the cryptic wisdom of 6.
To defeat the unique threat once and for all, 9 resolves to sacrifice himself to reclaim the talisman. In a heroic twist, 1 redeems himself by sacrificing his own safety to save 9. With the talisman now in hand, 9 manages to reabsorb the stolen souls of his friends, obliterating the Fabrication Machine for good. After this monumental victory, 9, 7, alongside 3 and 4, successfully release the souls of their fallen comrades from within the talisman. As they bid farewell to their friends, they ascend into the sky, heralding a new dawn for the world as the rain cascades down, infused with glowing bacteria, signaling the rebirth of life on Earth.
