Suppose Bryan wants to say "If you do that, then (i) I will leave, (ii) I will never go back, and (iii) I do not want to see you again.". My question is how to use punctuation to prevent the enumerations (i), (ii), (iii)? My guess is to rewrite it as "then I will leave; I will never go back; I do not want to see you again.". Is this understandable without causing confusion in the sense that the reader could get it that the idea is there are three consequents? Should I use commas instead of semicolons?
You have correctly used the semicolons, since each of your enumerations in a complete sentence. And your sentence is clear, forceful, and understandable. Nicely done, not everyone can use semicolons correctly!
As you suggest, however, using commas can simplify the statement.
If you do that I will leave, never go back, and I will not want to see you again.
The new sentence is more conversational, easier to read, but not as forceful as your semicolons.
The three parts are quite different in structure, and that makes it difficult to use uniform punctuation. As the sentence stands, I would combine the first two and make the third a separate item.
If you do that, I will leave and never come back, and I do not want to see you again.
Note that I have omitted then as it is rarely used in informal English, and have replaced go back with come back: when you leave, you have to come back, not go back. This sounds overly complicated though, and I don't feel comfortable about the do in do not want: I feel that it should maybe be a will in a conditional.
It would be easier if you rationalised the conditional clauses:
I will leave
I will never come back
I will never see you again.
You can then parallel them up like this:
If you do that, I will leave and never come back or see you again.
What you have are 3 distinct independent clauses. There are various ways to combine or not combine them.
You could make them separate sentences.
I will leave. I will never come back. I do not want to see you again.
You could combine them with semi-colons:
I will leave; I will never come back; I do not want to see you again.
I'd advise against this in this case. Generally combining more than 2 independent clauses with semi-colons sounds like a run-on sentence.
You could combine them with one or two conjunctions:
I will leave, I will never come back, and I do not want to see you again.
I will leave and I will never come back and I do not want to see you again.
The first is more common. It depends what rhythm you want.
You could also combine the common parts of the clauses:
I will leave and never come back or see you again.
Side note: I have a problem with combining "If you ... then I will" with "I do not want". The first two things are conditional: if you do this, then I will. But the third part is absolute, I do not want. I think it would make more sense as, "I will leave. I will not come back. I will never see you again." Or as this appears to be a threat, maybe "You will never see me again."
An alternative is to use a colon to introduce the series and semicolons to separate the items in the series. "If you do that, then: I will leave; I will never go back; and I do not want to see you again." This gives a greater impression than commas of an emphatic declaration with pauses to give greater weight to the individual parts.