A fantastic brain surgeon, Kenzo Tenma, helps people, he's called from a patient he's operating on one day to operate on a patient who's reputation will profit the hospital more. The man Tenma was operating on dies the next day. The wife yells at Tenma and asks "Why did you leave him?!"
Tenma is utterly shocked by what he had done but the fire is only fueled when the woman he's dating says that "All lives are not equal." and her father, the hospital Director says that helping the famous is more important than helping the lives of those in general. The next day a little boy with a bullet in his head comes in. He's going to die unless he gets immediate treatment and Tenma starts operating on him. Tenma is called away to help the Mayor after he got into some danger and Tenma refuses to go and stays with the boy and saves him, however the Mayor dies.
Tenma's status is stripped, his girlfriend leaves him, and the director tells him he has no chance of advancing in the medical world because he chose to save the child. Tenma only has the little boy he saved, Johan. He talks to Johan while he is still passed out and when the Doctor now takes Tenma's rights from seeing his patient away from him to get some publicity out of it the boy wakes up and poisons the Director and some others. Tenma is promoted to director and his life gets better.
11 Years later, Tenma is treating a patient who claims to have "Live after seeing a Monster." The patient runs away and is killed by this Monster. This Monster turns out to be none other than Johan, the boy he saved all of those years ago. The rest of the story is about Tenma and others finding Johan and killing him to end this. Johan just wishes to die but the people who worship Johan won't let that happen because some see him as the next Hitler and want him to rule, some see him as a God, and some are just utterly influenced by his charisma.
It's a really complex story.