Where would you put the germ of the Protestant Reformation?
Mainly political.
First of all, there was always politics and dissent within the Church as to be expected with pretty much any organization, and even Paul warned the Flock to be wary of those who sow division.
Secondly, there was always political conflicts within Europe and elsewhere, and it had long been the role of the Church to try and work out peaceful solutions. However, once countries split along with their new denominations, such a role became next to impossible, and the Wars of Religion plagued Europe for many decades and tensions stayed longer yet.
Thirdly, Jesus, the Apostles, and those whom they appointed referred to the Church as being "one body", but with that "one body" fragmenting into thousands of bodies with each feeling it's the only "true church", Jesus' and the Twelves' teachings have been betrayed.
But we should also remember that Joe & Mary Schmoe sitting in the pews are also very much part of the Church, and that has persisted for almost 2000 years, and there are a lot more of them than there are denominations and heads of denominations and churches, so not all is lost.