Honestly, while I liked Callisto, the ending fell flat for me. So I hope you at least get the ending done better for this one, If I like a character I want an ending with one of them.
Hardest parts of writing a story: The beginning and the end.
Especially the ending is difficult, but it is one of the first things a writer should sketch out. It will mean the writer won't have to worry too much about the ending, because he already has the outlines, but it also gives the writer a goal for the rest of the story, greatly reducing the chance for him to write himself into a corner or driving the story off-rails. With VNs, the problem is that there are usually several endings, and it's hard to keep the story consistent for all those endings. But, it pays off. It just requires the different storylines not to diverge too early or too much, as that exponentially increases the workload on the writier, increasing the risk that one or more endings get written off, or that development won't ever finish.
The beginning is almost as difficult. If you don't have a vision or direction for your story, then it's easy to start a story with a "one morning you wake up and go to work/school/whatever". But, if you have a direction for the story, it is terrible, as it won't give your character the background that you want to give him or her.. In that case, you'll usually want to introduce the character in a situation giving some background, like, in transit (meaning the character is closing a past), at work/school (giving information about the characters' skills and personality) or busy with some activity like sports or a hobby (giving information about the characters' secondary skills and interests).
Sometimes it works to have multiple introductions within a story, in which case the protagonist is usually the second introduction, while the first introduction either introduces an antagonist (doing something that starts the ball rolling for the protagonist), or the environment (introducing the time, the theme, the circumstances, and hinting at the main plot).
I said that the protagonis is usually second to be introduced, but sometimes the protagonist is already revealed, but not yet introduced. This can be something like an undescript character turning on the TV and then focussing the story on some news item, or the main character being a background or side character on an antagonist or environment introduction.
If you look through your favourite movies, I bet three out of four start with multiple introductions, and set the stage before introducing the protagonist. Most of them probably also already had a goal or a crude outline for the ending(s) before the beef of the storyline got any. The story is about the journey, not the destination. But to make the journey and thus the story worthwhile, the destination will need to be logical and acceptable as well.