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Source: https://writers.stackexchange.com/a/32472
License name: CC BY-SA 3.0
License URL: https://creativecommons.org/licenses/by-sa/3.0/

While not a program I would suggest using a [flowchart](https://en.wikipedia.org/wiki/Flowchart).

> A flowchart is a type of diagram that represents an algorithm, workflow or process, showing the steps as boxes of various kinds, and their order by connecting them with arrows.

Since you mention visual novels in your question 2 good examples I know of are the flowcharts that you can find for the translations of the visual novels _Tsukihime_ and _Fate/Stay night_.

[![Fate/Stay Night flowchart](https://i.stack.imgur.com/AHKUF.png)](https://i.stack.imgur.com/AHKUF.png)

While not the full image of _Fate/Stay Night_'s you can track down the original .pdf file (it's included in Mirror Moon's translation of the original game and the Realta Nua PC Translation (the latter is what I'd recommend)).

You can see how the flowchart can not only track progress, but also allows you to play with choices and variable management during planning for branching storylines ie. in _Fate Stay Night_ you see how it shows where it branches at the end of the 3rd day and that there is a check to see if you continue with the Fate Route (Blonde<sup>1</sup>) or Heaven's Feel Route (Purple).

As for a program you might want to try [yEd](https://softwarerecs.stackexchange.com/a/36206/148). The link there takes you to the Software Recommendations SE Site where I asked for software for making Character Relationship Maps. In a way Character Relationship Maps are very similar to flowcharts and using yDe myself I can say that you could make a flowchart similar to _Fate/Stay Night_'s in it.

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<sup>1: I say Blonde because the route colours match to the heroines who Shirou becomes romantically involved with. Fate = Saber who has Blonde hair, Unlimited Blade Works = Rin who generally wears Red, Heaven's Feel = Sakura who has Purple Hair</sup>

Original score: 8