An independent clause and a sentence are the same thing. And the first rule of all punctuation is that a comma goes before a coordinate conjunction that connects independent clauses. The fact that there are words in an independent clause that refer back to the first clause makes no difference.
There is, however, a very sophisticated rule that not a lot of people know: When a modifier that modifies BOTH clauses comes at the beginning of the sentence, the comma is omitted.
…When he showed me the letter, I was interested but I was not convinced.
…In the interim between now and two months from now, he will do research and he will come up with a plan.
Since the opening clause in the first and preposition phrase in the second modify both sentences, the comma is omitted.