Any answer is going to depend on exactly what you’re doing. Details matter.
While you can fudge calls to macros from JavaScript, this is one of the cases where doing so is unlikely to do you much good—unless you only want side-effects, which I’m assuming is not the case.
In general, you’re probably going to want to use the <jQuery>.wiki() method. Exactly what you’ll need to do depends on what you’re doing and where.
As one example. If you’re running some code within a <<script>> macro and want to include another passage as part of your code:
<<script>>
/* other code… */
$(output).wiki(Story.get('your passage name').processText());
/* more code… */
<</script>>
That will output the passage, “your passage name”, within the currently rendering passage at the <<script>> call site, just as though you’d used <<include>> instead.