You might want to use an object (JSON object, in Java they're called hashmaps, I think) instead of an array for better performance, lookups in arrays are a bit slow. The left part of a JSON object is usually called a key, so I think it fits the purpose. The file would look like this:
{ "script":{ "001-01":{"scriptLines": ["encounter 1, scene 1", "hi"]}, "001-02":{"scriptLines": ["encounter 1, scene 2"]}, "002-01":{"scriptLines": ["encounter 2, scene 1"]} } }
An alternative option would be using nested arrays, i.e.
{ "script":[ [ {"scriptLines": ["encounter 1, scene 1", "hi"]}, {"scriptLines": ["encounter 1, scene 2"]} ], [ {"scriptLines": ["encounter 2, scene 1"]} ] ] }
This approach might be better because you don't need to order the scenes manually and accessing array elements directly (when not having to loop through the whole array) is faster than using objects. The downside would be having to stick with numbers as encounter IDs, which could be a bit annoying with a larger amount of different enemies.
Sorry if I'm being obnoxious, I'll just shut up if you don't want that kind of feedback.