Oh! I assume you're talking about a trial only case. I always write out a "walkthrough" for the trial segment before I script anything "final". It includes testimonies, the correct answer for every evidence present and contradiction, all evidence descriptions, notes on major story points that I want to come out at a specific time, and notes to explain the flow of logic entirely. My method beyond that depends on the case.
Starting out, I focused almost exclusively on mystery and case logic elements. (Choosing to focus on either mystery-side or story-side while not paying much attention to the other is a good practice when you're starting out. There's a lot to learn, and it's easy to get overwhelmed.) I started with one idea I really liked, for instance, "Phoenix calls on Edgeworth to defend Trucy from a bank robbery charge shortly before Apollo Justice." I'd then brainstorm details about how the crime happened with rough ideas of what Edgeworth needed to figure out and when. Then I went to the walkthrough and then I went to the script.
The case idea I have in mind now is more character-focused, which requires a different approach. Now I have to work out where I want the characters to start and end up, how they're going to get there, how the characters will react to the events of the story, and whether those are building up to the story I want to tell or not. In my case, I'm also trying work out the mystery at the same time. Again, I don't recommend that for a new author. Then I'll go through my usual walkthrough and script pattern.
Hopefully that helps.
[D]isordered speech is not so much injury to the lips that give it forth, as to the disproportion and incoherence of things in themselves, so negligently expressed. ~ Ben Jonson
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