It's a Great Man story, which also chafes, but I certainly don't know Japanese literature/film/art/pop culture well enough (or at all, with the possible exception of a few corners of film) to know if it's intended this way or even carries the same connotations for its native audience.
Three generations of Steam family rush the whole world into the technological age under the whip of the Evul Overlords, the (American) O'Hara Foundation. The Steam F1 generation starts out wearing the human face of genius. His father (Steam F0) is pushing himself, his workers, and the environment (in Alaska, "Russian America") to unethical, unsafe, and destructive lengths to harness his phlebotenum in Jar C (highly compressed steam at low temperature or something like that). Steam F1 is disfigured in an accident while saving the workers, his father, and (presumably) the research.
We then move back to England to get Steam F2 (Steamboy his own self) involved in the plot. Steamboy (having taken part in a parallel salvation mission at the factory where he works) receives a mysterious package from Steam F0 with warnings that the contents are, under no circumstances, to fall into the hands of the O'Hara foundation. Hot on the heels of the Speedy Delivery, Clan Steam are the victims of a mysterious home invasion by agents of the O'Hara Foundation (who all seem to be very stereotypically British, despite the Foundation being the allegorical stand-in for America, Capitalism, and War-Mongering).
The crime is interrupted by the arrival of a wild-eyed Steam F0, who delivers news of the death of Steam F1, and urges Steam F2 to run run run and get the "Steam Ball" (for 'tis the contents of the package) to Mr. Stephenson. Chases ensue, and Steamboy briefly looks as if he will be rescued by Mr. Stephenson and his vaguely Niles-ish assistant. We spend enough time with Mr. Stephenson to learn that he, too, is a Great Man and a former rival of Steam F1.
Ultimately, Steamboy is taken captive and we learn that the rumors of the death of Steam F1 have been greatly exaggerated. He's just been resting up and working on his Superfly SteamPunk Skywalker arm, Phantom of the Opera (and they go the whole nine yards with that visual metaphor, believe you me) mask, and natty dreads. You know, in case the theme of the isolation of the Great Man was conveyed too subtlely for the groundlings.
At this point in the film, Steam F0 is the heel dragger who knows that the world is not yet ready for greatness; Steam F1's near-death experience, in contrast, has converted him into the embodiment of the "Baldrick, do you mean 'How did the War Start?'" conversation from Blackadder Goes Forth. When he's taking a break from teaching himself how to walk and feel pain again, he's created Steam Tower (BRANDING is everything), which he believes will---do something good for all people. Steam F2 is understandably confused by his philosophically schizophrenic (yet weirdly allegorical in their rigidity) role models.
He eventually escapes Steam Tower with one of the three Steam Balls in tow. He delivers this to Mr. Stephenson who is out for a pleasure cruise at night, through eel-infested waters, on a Royal Navy ship. Mr. Stephenson assures Steam F2 that the purpose of science is "To make people happy." Steamboy hands over the ball and Mr. Stephenson reveals himself to be a raving loony of a Great Man who worships The Nation as the foundation of happiness.
Arms-craving stereotypes from around the globe show up and the world's biggest science fair devolves into full-out SteamPunk war with a denouement to rival that of AI (this is not a flattering comparison for those of you fortunate enough to have missed that travesty).
I find myself in need of the external Hard Drive known as The Lovely A. There's an image in Virginia Woolf's fiction--Orlando, maybe---of a woman standing at window, watching shadow fall over the landscape, and it ends with something along the lines of "The 20th century had begun." I'm not sure why the confused wreck of London with a more intricately drawn Legion of Doom Scrubbing Bubble bobbing on the Thames brings that image to mind. Something about the darkness before the dawn of the era into which we poor sods may now be witnessing as we tread along in the wake of Great Men. All in all, it left me in dire need of a historical-political lie down. And I pass the incoherent savings on to you, the reader.