Following a war between humans and machines, the world is now in full post-apocalyptic mode, with all humans dead and only one mechanical beast still operating. It's intent on hunting down and killing a number of animated rag doll type figures that scurry about through the wreckage. The last to come alive is #9 (voice of ELIJA WOOD), who doesn't know who or where he is, and hopes to find answers from #2 (voice of MARTIN LANDAU), a similar rag doll.
Yet, the four-legged beast comes after them and leaves with #2 in its mouth after also trying to get #9 who's then rescued by #5 (voice of JOHN C. REILLY), yet another doll, this time a scaredy cat who returns #9 to the figures' hideout. Their leader, #1 (voice of CHRISTOPHER PLUMMER), isn't pleased by this development, and makes sure his enforcer, the hulking #8 (voice of FRED TATASCIORE), gets that point across. That's all while #6 (voice of CRISPIN GLOVER) comes off like a deranged artist, repeatedly painting the same strange symbols time and again.
Even so, with #9 certain that #2 was still alive when he was carried off, the latest numbered one sets off with #5 on a rescue mission, eventually teaming up with ninja-type warrior #7 (voice of JENNIFER CONNELLY) and later mute twins, #3 and #4 who catalogue everything they come into contact with. But #9 then makes a horrible mistake by placing a small device -- that he first found when he came to life -- into what looks like the appropriate slot, not realizing the ramifications of doing so.
Just then, a monstrous-sized, spider-like mechanical beast is reactivated, and not only tries to kill the numbered figures, but also manufactures other mechanical creatures to do the same. From that point on, the numbered figures try to avoid harm -- including having their souls sucked from their bodies -- while attempting to defeat their latest nemeses.