NOTE: This spoiler was sent in by Rahul
The movie starts off with The Scientist (Alan Oppenheimer) making a sapient ragdoll, on whose back he writes "9". Outside, the world is pretty much destroyed. A while later, when all is silent, 9 comes to life. Looking around, he sees the place ("the First Room") is a mess. He opens window and sees the entire city in ruins. He tries to say something, but nothing happens. He can't talk.
He walks with no little trepidation through the desolate, deserted city. He comes upon a car on the road. He looks inside and sees a mother and her child inside, dead. Recoiling from the sight, he hears a sound and sees a slowly-approaching light.
Hiding behind some ruins, he picks up a metal bar and waits. As the light comes closer, he swings the bar towards it and connects. When he looks at what he hit, he sees a creature very similar to himself, only slightly aged and differently crafted. He also has a small candle fitted to his headgear and wears a magnifying glass in front of his eyes.
The other creature ("2") (Martin Landau) sees him and gasps. 9 starts to run, but 2 calls out, "Wait! I'm a friend." 9 stops and goes to help 2 up. 2 gives 9 an appraising look and approves of 9's detail and design. When he sees that 9 can't talk, he (2) tells him to follow him. They go over to a discarded doll on the road, where 2 proceeds to look inside it. 9, in the meantime, picks up a bullet and plays around with it, unaware of what it is. 2 finds the doll's "voice box" and stops 9 from causing any damage with the bullet. He tells him that some things are better left alone. Then he inserts the voice box into 9's chest cavity (through the zipper). After some adjustment, 9 speaks (as Elijah Wood) and says, "Friend."
2 notices something inside 9 and pulls it out. It's a small hemispherical device ("The Talisman"), which has three shapes on it. He says that "he's" always drawing this (we find out later). 9 asks if they're alone. However, a loud sound answers that question. 2, afraid, instructs 9 to hide inside a broken can nearby. Standing outside, armed with a spear, 2 waits tensely for the "beast" to attack. He's attacked by a Cat Beast. The Cat sees the Talisman and takes it. He notices 9 inside the can and tries to attack him. With its claws inches from 9's face, 2 distracts it. The Cat swallows 2. When it looks inside the can, he sees it's empty. It leaves. 9 emerges from a different hiding place. His left arm is ripped a bit. He faints. His unconscious form is noticed by a one-eyed ragdoll ("5").
When he awakens, he sees 5 tending to him. His arm has been fixed. They're indoors now. 5 (John C. Reilly) tells him that 2 is better at fixing them, unaware of 2's fate. At that moment, an elderly, domineering ragdoll ("1") (Christopher Plummer) enters, angrily. He looks over 9 and yells at 5 for almost leading the beast to them. Another ragdoll, a huge one named "8" (Jphn Tatasciore) comes in. He's like 1's right-hand man/bodyguard.
1 orders all to go to the upper level. They go up in a bucket. At the top level, 9 sees they're in a half-destroyed church of some sort. A fighter plane has crashed into a part of the church. 1 narrates the story as he knows it. When he awoke, there was a war between man and machine. In a major battle, as the ragdolls ran for their lives, 5 lost his left eye and was saved by 2. The machines deployed poison gas bombs, that pretty much killed all life on Earth. Only things left were the ragdolls and the beasts.
1 tells 9 of all the ragdolls that have been lost - 3, 4, 7 and, now, 2. He orders 5 and 9 to go to watchtower. In another room, we see "6" (Crispin Glover) drawing the same shapes as on the Talisman (he's the one 2 was referring to). On the watchtower, they look through a telescope. 9 sees a large factory in the distance, with 3 towers. He says that that's where the Cat beast took 2. 9 wants to go there to rescue 2, but 5 is reluctant. When 9 says that 2 would have tried to save him, 5 relents. 5 has a map which they can use to get there.
As they walk towards the place, they find 2's headlamp. 5 wonders why he was out there all alone. They look for a tunnel. Suddenly, there's a huge sandstorm, which blows the map away. They can't go back. When the sandstorm recedes, they notice a huge footprint on the ground - the Cat Beast's. Needing light, they take a small lightbulb from inside a wrecked jeep's headlight. 9 fashions a small staff-torch with it. 5 says sadly that 2 was just like him.
In the distance, the shadow of a creature (with a beak?) finds 5's map.
5 and 9 reach the factory. It's a dark, imposing industrial place. They turn off the light and go inside. They see a cage and see 2 inside it. At first, 2 doesn't respond, but slowly awakens, happy that they came for him. They hear sounds coming from nearby. 9 takes a look and sees the Cat Beast there, trying to insert the Talisman into a socket. Suddenly, it hears a sound and sees 9. It attacks them. Just then, a beaked creature attacks the beast. It "kills" it, by beheading it. The creature removes its beaked headdress, to reveal that it is a female ragdoll - "7" (Jennifer Connelly). 2 and 5 are ecstatic to see her, as they thought she was dead. They introduce her to 9. In the midst of the happy reunion, 9 picks up the Talisman and unwittingly inserts it into the socket. 2 sees it and runs to stop him, but is too late. He pushes 9 out of the way, as the place comes alive. Suddenly, a bright green light shoots out from the machine and strikes 2 in the eyes and mouth. It drains all his life force and the poor ragdoll hits the ground, lifeless.
Just then, the place comes live. 5, 7 and 9 don't have time to mourn 2. The Machine (a large sphere, with a bright red light in the middle, electrodes on its body and long limbs) comes to life. The surviving ragdolls run, but find themselves trapped at a chasm. 7 sees a lever switch overhead and uses 5's grappling gun to shoot a hook around the switch. 7 and 9 grab 5 and swing towards a conveyor belt on the other side. However, their collective weight causes the switch to be thrown and the resultant jerk causes 7 to lose her grip and fall, while 5 and 9 fall onto the belt. 7 manages to grab a ledge and hangs one-handed off it. The conveyor belt starts to move (due to the thrown switch) and 5 and 9 have to dodge many large metallic objects. They fall to the floor below. The Machine moves menacingly towards 7, sparking its electrodes. It gets distracted by 5 and 9's staff-light and chases them. 5 and 9 hide for a few tense moments as the Machine looks for them. 7 arrives and they run into a tunnel. The Machine is too large to chase them in the tunnel, so they manage to escape.
Outside, 5 is devastated about 2's death, while 7 is mad at 9. She knows where to find answers and tells them to follow her.
Meanwhile, the Machine uses the material around it to create a new monster.
5, 7 and 9 go to a destroyed library, which has a large courtyard with statues on it. They look at old paintings and see books scattered all over the place. 7 calls out and two twin ragdolls show up ("3" & "4"). They're mute, but their eyes can project memories. They look over 9, analyzing him. 7 asks them for help saying that they awakened something terrible. 9 guiltily corrects her that HE was the one who awakened it. Using their eyes, the twins project a video on a book, which tells about the Machine. The Machine was made by the Scientist, under orders from the dictatorial Chancellor. It was called the Brain. It has the ability to create its own machines. They used it in a war, but soon it turned against Man and, pretty soon, the world was destroyed.
Eager to know more about the Talisman, 9 draws the three shapes. 5 says 6 draws those very shapes. 9 says he wants to see 6, however 7 doesn't want to return (she doesn't like 1 very much) and runs off.
5 and 9 return to the church to see 6. However, 8 grabs them. 1 enters, mad as hell. He accuses them of dooming them all. 9 asks who sent 2 to scout outside, and 1 answers it was him. 6 comes in and sees the shapes drawn by 9. He says that the shapes are the "Source". 9 wants to investigate further, but 1 orders them locked up. 9 calls 1 a coward. 1 angrily says he'll do what it takes to keep them safe.
Just then, the church is attacked by the newly-created Bat Beast (bat wings, long beak). They flee for their lives, as the place starts to catch fire from the beast's attack. They wind up on the wing of the crashed plane. Just as they're cornered, 7 enters and tries to attack the beast from behind, but the beast turns and swats her away. She tries again, but it shoots a cabled harpoon into her leg. It starts to reel her in, but 9 grabs her and stabs her spear into the wing, arresting their movement. 8 cuts the taut cable, which causes it to swing away and wrap around a blade of the wing's propeller. Due to the tussle on the wing, it starts to slowly slide downwards. 8 grabs a groove in the wing. 7 holds on to the embedded spear, while 9 holds on to the harpoon in her leg. 1 loses his balance and his staff. 9 grabs the staff and holds it out for 1 to hold on to. 5 and 6 land in the propeller mechanism. They turn on the propeller. The spinning propeller starts to pull the Bat towards it, but, with a burst of strength and speed, it jumps and, landing inches away from 1, grabs his cape with its beak. 9 yells out for 1 to let go of his cape. Reluctantly, 1 releases the cape, causing the beast to snap back into the spinning propeller. It gets torn apart.
However, the ragdolls are now homeless, thanks to the fire. 1 watches sadly as their sanctuary burns down. They go to the library (where 3 and 4 live).
A drone takes the destroyed Bat Beast back to the Machine. The Machine is angry. It looks at 2's body and seems to get an idea.
At the library, 8 is appointed as the lookout. It's all quiet outside. He uses magnet on his head to get some sort of a high.
While 3, 4, 6 and 9 go over the shaped, 1 is upset about what he terms "dark science". When 9 accuses him of letting 2 die, 1 says indignantly that 2 was sacrificed as he was old and weak. Furious, 7 jumps on him, knife at his throat. But 9 talks her down. Angrily, she walks off.1 leaves as well, angry. 9 wants to go to scientist's place (the First Room).
Outside, 8 hears some sounds and looks around. He walks tensely through the courtyard. Suddenly, he sees 2. 2 rises up and his eyes start flashing hypnotically. 8 gets mesmerised.
In a different room, 1 walks in a huff. He hears a sound and gets scared. His fear increases tenfold, when he sees 2 floating towards him. Just like 8, he too gets hypnotised by 2's flashing eyes. Attached to 2 is the tail of a Snake Beast (with a one-eyed skull, fabric-covered body and jointed legs, with sharp objects on them). It picks up 1 and starts to tie him up. 8 has already been stuffed inside the Snake. As the snake starts to reel in the unconscious 1, 5 and 9 run up. The Snake sees them and holds up 2 (with flashing eyes) in front of them. While 9 averts his eyes, 5 gets hypnotized, standing rooted to the spot. Just then, 7's spear hits 2 and embeds him in a wall nearby, stopping the hypnotic flashing. 7 runs towards 2's body, dodging the Snake's attacks. Retrieving her spear, she cuts the Snake's tail off, thereby freeing 2's body. The Snake grabs her and is about to kill her, when 5 snaps out of his trance and shoots the Snake in its good eye. The Snake starts to slither away with 7 and 8. 7 screams out to 9, who runs after it. But the Snake gets away with the two ragdolls.
1, however, has been rescued. 9 tells 1 that the Snake has 7 and 8. He demands that they go save them, but 1 refuses. 9 persuades him. They give 2 a fitting funeral, putting him on a raft, with a coin on his eyes, and let him float freely into the sewer.
They set off to the factory. Taking the staff-light, 9 goes inside alone. He tells 5 that if he doesn't return, he (5) has to destroy the factory. 5 tells the others to look for a drum of fuel.
Inside the factory, 9 sees the Snake hand 8 over to the Machine. 8's life force is drained by the Machine, which gets more powerful. The Snake then starts to hand over 7. 9 ties a cable around a bolt and throws the bolt onto a ledge, behind a pair of moving cogs. He then distracts the Snake. Putting 7 back inside itself, it chases after 9. Through it's one broken eye, it sees what it takes to be a ragdoll. It grabs it and starts tying it up. Actually, it's a piece of ragdoll fabric wrapped around the staff-light, which 9 holds while in hiding. The Snake suddenly turns on the lightbulb and recoils. 9 burst out of hiding and starts to run, knife in mouth. The Snake sees 9 and gives chase. The dummy ragdoll is connected to the cabled bolt. As the Snake slithers after 9, it pulls the cable, which gets caught in between the cogs. The cogs start pulling the cable, which yanks the Snake backwards towards the cogs. Turning, 9 races after the Snake. As the Snake gets pulled upwards, he runs up its fabric body and plunges his knife into its body and slides down, ripping open its body. 7 falls free into 9's arms below. The Snake's head gets crushed in between the cogs.
Outside, the ragdolls prepare to push a barrel inside the tunnel. 1 is all for getting it done immediately, but 5 wants to wait for 7 and 9. They are noticed by a recon drone. Using 5's grappling gun, they rope it and start to pull it towards them.
Inside 7 and 9 are seen by the Machine, which sends mechanical spiders after them. 7 and 9 sprint into the tunnel and yell for the ragdolls outside to send in the barrel. 1 and 5 push the barrel (which has a lit fuse) into the tunnel. They've also connected the cable (which they've tied around the drone) to the barrel. As the barrel (and drone) rolls down the tunnel, 7 and 9 run around it. The barrel knocks back all the spiders and falls inside the factory, where the Machine can only watch helplessly as it explodes. The factory erupts in flames, as the ragdolls escape.
The ecstatic ragdolls start to celebrate. 3 and 4 put on a record player. 1 feels a bit downcast. As 5 chases a runaway LP record, he notices, to his horror, that the Machine is still alive. It chases him. 9 tries to run to his rescue, but 1 restrains him. The Machine grabs 5 and drains his life force, regaining its strength.
The ragdolls run towards a rickety bridge, with the Machine behind them. 6 notices that the dead ragdolls' souls are trapped inside the Machine. While they run easily across the bridge, the Machine is too heavy and the bridge gives way under it. It tries to pull itself up. 6 tells them not to destroy it, else their fallen comrades will be trapped forever. The Machine falls, but grabs 6 on the way down. 6 yells for them to go to First Room for the source. The others watch helplessly as the Machine drains him.
9 wants to go to the First Room to find out more on how to save the trapped souls. But the others want to destroy the Machine.
9 runs off to the First Room (where he was made). There, he sees schematics for the Machine and the ragdolls. He notices a holographic projector marked "9". He turns it on and a hologram of the Scientist comes on. The Scientist tells 9 about the Machine. While the Machine is made up of the Scientist's life force, the ragdolls are all pieces of his soul. He shows 9 the Talisman and a sequence in which to turn off the Machine. 9 was his last ragdoll before he died, drained of his own life force.
9 runs over to others, who are busy hurling bombs at the rapidly advancing Machine. 9 tells them that the Scientist is the Source. However, 1 continues attacking the Machine. As the Machine approaches, they run. The Machine gets stuck in some barbed wire, allowing the ragdolls to hide. 9 tells the others that they have to get the Talisman from the Machine. The Machine fires at them, causing a huge explosion. The ragdolls fall scattered around, bruised but alive. 1 however has lost a few fingers.
9 bravely goes to face the Machine. Just as the Machine is about to drain 9, 1 pushes him out of the way, sacrificing himself, losing his life force. 9 grabs the Talisman off the Machine. He hits the sequence and aims the Talisman at the Machine. The Machine screams at the souls are transferred to the Talisman. Now soulless, it explodes.
3, 4 and 7 find 9, slumped on the ground. He's alive. 7 tells him he did it, but he responds "not yet".
They light a fire and set 5 positions around it for their 5 fallen comrades, with the respective numbers on them. 9 hits the sequence on the Talisman. One by one, the souls are released. 8 is the first one out. He smiles at them. 6 comes out next. Taking 8 by the hand, he leads him to his place. 2 and 5 come out together. 1 is the last one out. He gives 9 a grateful nod and they all go to their respective positions. 5 lingers a bit and looks at 9. Then, they all float up to the heavens, finally free. It starts to rain. 3, 4, 7 and 9 are left below. 7 asks 9 what will happen now. 9 answers he's not sure what happens next, but this world is theirs. It's what they make of it.
The rain drops hit the "camera" and then the viewer sees a closeup of the water showing microorganisms thriving in the water droplets. This indicates that life will once again flourish in the world, though rather slowly and over time.
Thanks for the added info, Melissa...