Johans motivation

After thinking about it another night, more aspects fell into place.

There are a lot of parallels within the story, which show the different options and attitudes.

1. Some people have mentioned, that it isn't made clear enough how the "evil power" of Johan works. It's true that while we see Tenma and his friends doing a lot of good things, Johan seems apparently to remain vague. However, I think we are given enough information nonetheless. As opposing forces (or so it seems until the end) Johan and Tenma (but also Grimmer, very important in this respect) are working in very similar ways: by encouraging people. The key to understand it is the book of the "monster without a name". The monster offers to make people strong, and keeps its promise, but devours them in the end. Johan encourages people to do things by bringing out their dark aspects; he makes his sister shoot him, the children in the orphanage to start a rebellion, Karl to finally meet his father, the children playing "suicide-games", etc.
It's the same way Tenma - but I think in those few scenes even more Grimmer - are working their "good powers": they too encourage people, but in a different way that not leads to self destruction in the end.

2. The symbolicism of the monster story applies very well to Johans way of seing things. The monster splits up (a referrence to the twins), but in the end one devours the other again. As mentioned above, it seems that Johans actions are largely motivated by the feeling of guilt towards his sister. The monster was one, before it splitted up, and so he feels with the things that happened to his sister, but also as being the reason for her misfortune. He tries to erase all those people responsible for that, but in the end, also himself as the main cause.

3. I have another hypothesis concerning the ending, that might explain things, where some folks wonder whether Tenma is just stupid not shooting Johan in the end or even helping him.
The reason (as I understand it) for the ending is, that the characters finally get into place they belong to (in terms of story telling). What do I mean by that?
The whole story Tenma is chasing after "the monster", and both him as well as Johan believe, "the monster" and Johan are identical, making Johan the Antagonist. I think that's not the case. I think Johan is in the end more a Contagonist, which is a character that gets into the way of the Protagonists to lure him from his objective. The Contagonist has an impact on the Protagonist - he can either change or remain steadfast through this encounter. The Antagonist also can be something more abstract, and in this story I think the Antagonist or goal can be defined as "making the bad things undone/ terminating the cause of it all". However, the cause here isn't the person, at least not Johan, who is a monster - that's what we ultimately learn; it's the decision to make experiments with human beings, to deprive the children of love and identity/ a name they can identify with etc. (since they are supposed to work for the sole purpose - hitman, spy etc. - they don't get an identity that interfers with their function). That's why the Protagonist (Tenma) can't "solve the puzzle" by killing another person; he has to put a force against the destructiveness those experiments and inhuman behaviour caused in Johan as well as in other people.
Tenmas objective is to kill "the monster" - which means "the cause of all of this". But during his journey he discovers all those cruel things that happened, and we finally come to understand Johan hasn't been the reason, albeit he behaves like the monster and other people call him so.
The episode "The True Monster" shows us what was setting those things in motion; some folks argued, the mother might be the "real monster", but she isn't; she's a victim herself. Her failure was to choose, when she couldn't have, but this wasn't a concious selection, rather hasty and full of doubts (which she passes to Johan). She thinks she has to decide for one, or both will be taken away. She is forced by Bonaparte and his experiments to choose, the most cruel act, which splits the twins and leads to Johans identification with the monster. However, Johan seems not to be the monster himself ("the monster inside me is about to come out" - it reminds us of the sick prince in the story), but possessed by it.
Tenma want's to erase the cause, which is of course impossible to do with a gun; Johan is not the Antagonist, as he isn't going to kill Tenma, albeit he has a lot of chances, but Contagonist, as he tries to change Tenma in his nature: Tenmas main principle from beginning to end is to protect life. Johan wants to make him change his principles (so is the Joker in "The Dark Knight" trying to change Batman etc.) by making Tenma shoot him. He is trying to make Nina do the same, as he somehow sees both of them as victims (my theory). He kills on the other side all the people who appear working together with - or representing - the authorities and try to divide him from his sister.

This series gives me much to think about, albeit some things are not spoken out clearly. There are laid out a lot of hints that are suggesting a key to understanding. And keeping the thoughts occupied after one is done watching it is what makes art great, I think.