During a period of economic decline, the government of a totalitarian state commissions scientists to research ways for the nation to prosper. One scientist develops an artificially intelligent brain, but before it can be properly tested, it is taken away by the government to build the Fabrication Machine, which is used to labor for the people and create machines for war. Eventually the Fabrication Machine snaps under pressure and turns against humanity, programming its machines to eradicate all forms of life. During the chaos, the scientist who invented the machine's A.I. creates a mysterious talisman and a set of nine numbered ragdoll-like "stitchpunks," hoping they will preserve humanity's legacy and allow life to continue. He brings them to life by transferring his soul into each of them, and dies as soon as he gives life to the final stitchpunk, numbered "9."

9 awakens in the scientist's laboratory, the world now a barren wasteland, and finds the scientist's talisman, which he instinctively takes with him. While exploring the ruined world, he encounters another stitchpunk, 2, who tells him of others like themselves before he is captured by the Cat Beast, which steals the talisman and takes 2 towards a towering factory in the distance. 9 escapes the attack and is found by the group of other stitchpunks consisting of 1, 5, 6, and 8, who have all been hiding in fear of the Cat Beast. 9 explains what happened to 2 and insists they save him, but 1 refuses to jeopardize their safety. 5, on the other hand, is convinced to help 9. The two enter the factory and save 2 from the Cat Beast, which is decapitated thanks to the timely arrival of 7. Noticing a socket shaped like the talisman, 9 inserts the talisman into it out of curiosity, only to have it open and inadvertently seal away 2's soul, leaving 2 lifeless. This reactivates the long-dormant Fabrication Machine, prompting 9, 5, and 7 to flee.

Seeking answers about the Fabrication Machine and the talisman, 9 is taken to meet 3 and 4, who reveal details about the machine's past, though they know nothing about the talisman. 5 tells 9 that 6 might have answers and return to the hideout, where 6 states they must "go back to the source," where the talisman's secrets can be found. 1, however, berates 9 for awakening the Fabrication Machine and argues that 9 will just lead them to more trouble. Suddenly, the hideout is besieged by the Winged Beast, a new machine created by the Fabrication Machine. Through a combined effort, the stitchpunks destroy the Winged Beast, though the hideout is burned down in the process. During their search for shelter, they are attacked by another new machine, the Seamstress, which kidnaps 7 and 8 and nearly captures 1, who is convinced to strike back against the machines.

9 infiltrates the machine factory where he is able to save 7 and destroy the Seamstress, though he arrives too late to prevent the Fabrication Machine from taking 8's soul with the talisman. 9 and 7 escape while others ignite a barrel of gasoline and roll it into the gas-filled factory, causing the building to explode and apparently destroying the Fabrication Machine. As the stitchpunks celebrate, 5 wanders off to find the Fabrication Machine is still active, and barely manages to warn the others before the machine steals his soul. During the ensuing chase, 6 tells 9 that the souls of the dead stitchpunks are trapped inside the Fabrication Machine when he too loses his soul, but not before he urges the others to return to "the source" rather than destroy the machine. Despite this, 1, 7, 3, and 4 plan to destroy the Fabrication Machine anyway, believing the dead souls cannot be saved. 9 decides to heed 6's final words and returns to the laboratory where he first awoke and found the talisman, determining it to be "the source."

Back in the labortory, 9 finds a message from the scientist explaining how to use the talisman. When the others begin their attack on the Fabrication Machine, 9 returns with a plan to take the talisman back from the machine and use it to retrieve the souls, intending to bait himself to the machine and sacrifice his soul. 1, however, ultimately makes the sacrifice instead, allowing 9 to use the talisman to retrieve the souls, destroying the Fabrication Machine in the process. Afterwards, 9, 7, 3, and 4 set up a memorial for 1, 2, 5, 6, and 8. 9 opens the talisman and releases the souls, which scatter across the sky and bring life back to the world, leaving its future in the hands of the stitchpunks.

Stitchpunks

• 1, the oldest of the stitchpunks and their self-proclaimed leader of the tribe. He is clever and sly, but also domineering, irritable, quick-tempered and slow, if not unwilling, to trust 9. The Scientist described 1 as struggling out of his hands after his creation, and being stubborn and defiant. 1's skin is fastened by many metal snaps. He wears a tall hat and holds a peculiar staff with a small bell on it. Voiced by Christopher Plummer.

• 2, a kind, delicate old inventor. He is fascinated by junk, and he loves to explore the wastelands and look for parts for his inventions. His health is fading, is always walking with a cane, and can only see with a lorgnette. The Scientist wrote that after 2's creation, 2 began tinkering with the loose parts of the Scientist's workshop. 2's skin is fastened with many knotted strings. He wears a helmet that he built himself. Voiced by Martin Landau.

• 3 and 4, curious but shy twin stitchpunks. They are unable to speak, using flickering lights to communicate with each other, but when they need to explain things to someone else, their eyes turn into film projectors. They instinctively run and hide at the sight of danger. Both wear hoods. After the Scientist created them, they playfully romped around his workshop and read all of his books. It is possible that they are made from gardening gloves.

• 5, a healer, tutor, and skilled mechanic/engineer. He is the journeyman of 2, the great engineer and inventor. He is a diligent worker, a meek spirit, and a devoted friend. He is missing his left eye (lost years earlier in a Walker attack), instead wearing a metal plate. The Scientist remarked that 5 was the first of his creations not to run off or explore the workshop; instead, 5 was very trusting of the Scientist. He has buttons on his front to fasten his skin. Voiced by John C. Reilly.

• 6, an artistic, wild and impulsive stitchpunk. 6's fingers are made of ink pen nibs, which he uses to draw. He has prophetic visions of the past and future, channeling his visions through drawings to interpret them, which are accurate in predicting events and help solve mysteries that puzzle 9. The Scientist described him as being peculiar and unable to naturally fit in to his surroundings, judging from his expressive artwork that he sees the world differently from the other creations. One of his eyes is slightly larger than the other, and paintbrush bristles sprout from his head. Voiced by Crispin Glover.

• 7, a warrior. A rebel and a loner, she is willing to take many risks for the good of the stitchpunks. She is impatient and can be reckless and stubborn, but makes up for it with mobility and grace, caution of her surroundings, and calmness in dangerous situations. Her color has been bleached away by the sun. She uses a blade mounted on a long staff for fighting, and wears a helmet made from a bird's skull. The Scientist described her as being fiercely independent and created her to be a mediator that could manage the stitchpunks with ferocity and keenness. Voiced by Jennifer Connelly.

• 8, a giant, mean brute. He is 1's personal bodyguard and would die for him, though he is crude and mocking towards everybody else. He is strong and fierce, wielding two masterful weapons, half a pair of scissors and a kitchen knife used as a sword. The Scientist deemed him to be all muscle and intimidating, though none too bright. He uses a magnet to entertain himself. Voiced by Fred Tatasciore.

• 9, the protagonist. Good-hearted, thoughtful and sincere, he is always willing to risk his life to save others. Despite being a newcomer to the group, he displays leadership qualities that can help the others survive. He seeks truth in the history of the world and the stitchpunks, and wishes to know the meaning of life. 9 has a zipper on his body to fasten his skin. Voiced by Elijah Wood.

Humans

• The Scientist, a former toy-maker funded by the nation's Chancellor to build the B.R.A.I.N. Before he could properly test his invention, however, it was confiscated by the government and put to use immediately. Knowing the dangers of such actions, since the B.R.A.I.N. had no soul, the Scientist denounced the Chancellor and went into hiding, joining an underground group of rebels. When his worst fears came true, he hoped to atone for his part in humanity's destruction by creating the talisman and the stitchpunks, hoping they would preserve humanity's squandered gifts. One by one, he brought the stitchpunks to life by transferring his own life force into them, eventually dying at the beginning of the film. Voiced by Alan Oppenheimer.

• The Chancellor, a ruthless dictator who intended to help his nation prosper after the end of a very great war, and funded the Scientist in his development of the B.R.A.I.N. He used the B.R.A.I.N. to create the Fabrication Machine and put into labor for his people so they could lead leisurely lives. Eventually he declared war on the other struggling nations and forced the Fabrication Machine to build other machines for battle. This, however, pushed the Fabrication Machine beyond its limits, and it turned against humanity. He was eventually killed by his own war machines, reprogrammed by the Fabrication Machine. Voiced by Tom Kane.

Machines

• The B.R.A.I.N., (Binary Reactive Artificially Intelligent Neurocircuit), an artificial intelligence created by the Scientist for his country after a great world war as a display of the country's wealth and science. However, it was taken by the Chancellor of the country before it could be properly tested and placed inside the The Fabrication Machine, soon creating machines that ravaged the planet. B.R.A.I.N., was pressed to its limits by the Chancellor to build machines for war. It eventually snapped under pressure and was driven to wipe humanity off the face of the Earth. It had at least a dozen extra optical sensors on its head for multi-directional vision and a long tail, which is used to fixiate the machine to the ceiling of the factory, but is jointed so it may move around the factory to create machines from spare parts. When angered, electricity would arc over the surface of its head.

• The Cat Beast, an ape-like creature and also the first machine that 9 encounters. It resembles a cat skeleton and its head is made using a cat's skull. The Cat Beast has a red mechanical eye in its left socket and a light bulb in its right, which it uses to see in the dark. It uses its teeth and long, razor sharp claws to attack its prey. Its behavior out of all the machines seems to be the most feral. In the short film upon which the movie is based, this machine was the primary antagonist.

• The Winged Beast, a pterosaur-like machine. It flies with wings made from the nation's banner and a propeller, and its head and mouth consist of knives, saws, dental tools, and other razor-sharp weapons. It also contains a harpoon launcher on its tail to trap its prey.

• The Seamstress, a cobra-like machine with a broken doll's face covering its real one. It hides in the shadows and waits to draw its prey out with a lure on the end of its tail, which happens to be the stitchpunk 2. The eyes emit a blinking blue light which can hypnotize its victim before attacking with a set of insect like legs on its front. It then ensnares the prey by tying up the victim with one of three spools of red thread that it carries on its back, hence the name, and storing the caught prey in its belly.

• Zeppelin Beasts, large zeppelin or balloon-like machines with small bodies in place of a gondola. Zeppelin Beasts move via a pair of bellows at their rear and seem to be aerial patrols for the Fabrication Machine. They have two eyes on stalks and an air raid siren, which one uses to alert the Fabrication Machine to the stitchpunks' presence.

• Walkers, a machine seen mostly in old recordings. These tall machines stand on long legs and are equipped with a Vickers machine gun and mortar shells full of toxic gas.

• There are smaller, spider-like machines built by The Fabrication Machine to help with its work and guard the Factory.