Question

The Ninety-Five Theses, written by who questioned. This document was largely responsible for starting the what

Answer 1

The 95 Theses started the reformation.

Answer 2

Here's how to complete that sentence:

The 95 Theses, written by MARTIN LUTHER, question the CHURCH'S USE OF INDULGENCES.  This document was largely responsible for starting the PROTESTANT REFORMATION.

Details:

The official title of Luther's document, which he put forth on October 31, 1517, as theses for debate, was:  Disputation on the Power and Efficacy of Indulgences.  Indulgences were papers issued by the authority of the pope that granted the person obtaining them the removal of penance owed in regard to their sins.  Luther objected not only to the fact that these papers were being peddled for money, but questioned many of the doctrinal foundations behind the use of indulgences.

Additional detail:

What many people don't realize is that Luther had produced a set of 97 theses several weeks earlier, in September, 1517, which spoke against some of the core theological positions of the Catholic Church.  That document was called, "A Disputation against Scholastic Theology" -- in other words, the theology taught by the "scholastics" or "schoolmen" in the theology departments of the universities.  That document didn't attract a lot of notice initially, because it was the sort of doctrinal debate university types might have with each other.  But in October, 1517, when Luther wrote and posted "A Disputation on the Power and Efficacy of Indulgences," this document stirred up a firestorm.  It was attacking the money-making asset that indulgences had become for the church, and spoke to the concerns of many average people who felt they needed to pay for such indulgences to get themselves or deceased relatives out of the pains of purgatory.