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In a written medium, your readers can only identify your characters by what you give them. We cannot "see" your characters. So, if at any point in the story there's a John, and then again there's a...
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#4: Attribution notice removed
Source: https://writers.stackexchange.com/a/47674 License name: CC BY-SA 3.0 License URL: https://creativecommons.org/licenses/by-sa/3.0/
#3: Attribution notice added
Source: https://writers.stackexchange.com/a/47674 License name: CC BY-SA 3.0 License URL: https://creativecommons.org/licenses/by-sa/3.0/
#2: Initial revision
In a written medium, your readers can only identify your characters by what you give them. We cannot "see" your characters. So, **if at any point in the story there's a John, and then again there's a John, they're the same John, unless you give us something else to distinguish the two Johns.** "Something else" might be a surname. It might be a nickname. It might be that one is called John, while the other is Johnny. It might be that one is called, for instance, Long John, all the time. That's important - he isn't just Long John in that one scene with the other John - Long John is his "name" _all the time_. **You need to maintain the distinction between the two characters all the time, not just in the one scene they are together.** Calling a character "New John" because he appears later in the story is meta - it's a nickname related to a story feature, it doesn't make sense _inside_ the story. It's something you can only do if the narrator is also very much a character. By using a meta element, you're drawing attention away from the story, and to the act of storytelling. Thus it only makes sense if that's the effect you're deliberately trying to achieve. Otherwise you'd have to consider giving the two characters some sort of nickname or pet name or similar, that makes sense within the story. Then use that consistently as the character's name.