The only way to kill Doctor Manhattan
It's obviously you need to invent time mashine, go back in time and kill Jon while he is human and didn't become Doctor Manhattan.
True, but with Dr. Manhattan's ability to read future events, he would know what they were trying to accomplish before they did it.
shareBut with his acceptance of the flow of fate, he might not actually stop you. It has happened. He won't stop it because he doesn't/didn't/isn't.
And/or you could use the tachyon technobabble machine that Ozymandias used to cloud his ability to know what you were up to.